Yield-related polynucleotides and polypeptides in plants

ABSTRACT

The invention relates to plant transcription factor polypeptides, polynucleotides that encode them, homologs from a variety of plant species, and methods of using the polynucleotides and polypeptides to produce transgenic plants having advantageous properties compared to a reference plant. Sequence information related to these polynucleotides and polypeptides can also be used in bioinformatic search methods and is also disclosed.

This application claims the benefit of U.S. Non-provisional applicationSer. No. 09/837,444, filed Apr. 18, 2001, U.S. Provisional ApplicationNo. 60/310,847, filed Aug. 9, 2001, U.S. Provisional Application No.60/336,049, filed Dec. 5, 2001, U.S. Provisional Application No.60/338,692, filed Dec. 11, 2001, and U.S. Non-provisional applicationSer. No. 10/171,468, filed Jun. 14, 2002, the entire contents of whichare hereby incorporated by reference.

JOINT RESEARCH AGREEMENT

The claimed invention, in the field of functional genomics and thecharacterization of plant genes for the improvement of plants, was madeby or on behalf of Mendel Biotechnology, Inc. and Monsanto Company as aresult of activities undertaken within the scope of a joint researchagreement in effect on or before the date the claimed invention wasmade.

FIELD OF THE INVENTION

This invention relates to the field of plant biology. More particularly,the present invention pertains to compositions and methods forphenotypically modifying a plant.

INTRODUCTION

A plant's traits, such as its biochemical, developmental, or phenotypiccharacteristics, may be controlled through a number of cellularprocesses. One important way to manipulate that control is throughtranscription factors—proteins that influence the expression of aparticular gene or sets of genes. Transformed and transgenic plants thatcomprise cells having altered levels of at least one selectedtranscription factor, for example, possess advantageous or desirabletraits. Strategies for manipulating traits by altering a plant cell'stranscription factor content can therefore result in plants and cropswith commercially valuable properties. Applicants have identifiedpolynucleotides encoding transcription factors, developed numeroustransgenic plants using these polynucleotides, and have analyzed theplants for a variety of important traits. In so doing, applicants haveidentified important polynucleotide and polypeptide sequences forproducing commercially valuable plants and crops as well as the methodsfor making them and using them. Other aspects and embodiments of theinvention are described below and can be derived from the teachings ofthis disclosure as a whole.

BACKGROUND OF THE INVENTION

Transcription factors can modulate gene expression, either increasing ordecreasing (inducing or repressing) the rate of transcription. Thismodulation results in differential levels of gene expression at variousdevelopmental stages, in different tissues and cell types, and inresponse to different exogenous (e.g., environmental) and endogenousstimuli throughout the life cycle of the organism.

Because transcription factors are key controlling elements of biologicalpathways, altering the expression levels of one or more transcriptionfactors can change entire biological pathways in an organism. Forexample, manipulation of the levels of selected transcription factorsmay result in increased expression of economically useful proteins ormetabolic chemicals in plants or to improve other agriculturallyrelevant characteristics. Conversely, blocked or reduced expression of atranscription factor may reduce biosynthesis of unwanted compounds orremove an undesirable trait. Therefore, manipulating transcriptionfactor levels in a plant offers tremendous potential in agriculturalbiotechnology for modifying a plant's traits.

The present invention provides novel transcription factors useful formodifying a plant's phenotype in desirable ways.

SUMMARY OF THE INVENTION

In a first aspect, the invention relates to a recombinant polynucleotidecomprising a nucleotide sequence selected from the group consisting of:(a) a nucleotide sequence encoding a polypeptide comprising apolypeptide sequence selected from those of the Sequence Listing, SEQ IDNOs:2 to 2N, where N=2-561, or those listed in Table 5, or acomplementary nucleotide sequence thereof; (b) a nucleotide sequenceencoding a polypeptide comprising a variant of a polypeptide of (a)having one or more, or between 1 and about 5, or between 1 and about 10,or between 1 and about 30, conservative amino acid substitutions; (c) anucleotide sequence comprising a sequence selected from those of SEQ IDNOs:1 to (2N−1), where N=2-561, or those included in Table 5, or acomplementary nucleotide sequence thereof; (d) a nucleotide sequencecomprising silent substitutions in a nucleotide sequence of (c); (e) anucleotide sequence which hybridizes under stringent conditions oversubstantially the entire length of a nucleotide sequence of one or moreof: (a), (b), (c), or (d); (f) a nucleotide sequence comprising at least10 or 15, or at least about 20, or at least about 30 consecutivenucleotides of a sequence of any of (a)-(e), or at least 10 or 15, or atleast about 20, or at least about 30 consecutive nucleotides outside ofa region encoding a conserved domain of any of (a)-(e); (g) a nucleotidesequence comprising a subsequence or fragment of any of (a)-(f), whichsubsequence or fragment encodes a polypeptide having a biologicalactivity that modifies a plant's characteristic, functions as atranscription factor, or alters the level of transcription of a gene ortransgene in a cell; (h) a nucleotide sequence having at least 31%sequence identity to a nucleotide sequence of any of (a)-(g); (i) anucleotide sequence having at least 60%, or at least 70%, or at least80%, or at least 90%, or at least 95% sequence identity to a nucleotidesequence of any of (a)-(g) or a 10 or 15 nucleotide, or at least about20, or at least about 30 nucleotide region of a sequence of (a)-(g) thatis outside of a region encoding a conserved domain; (j) a nucleotidesequence that encodes a polypeptide having at least 31% sequenceidentity to a polypeptide listed in Table 5, or the Sequence Listing;(k) a nucleotide sequence which encodes a polypeptide having at least60%, or at least 70%, or at least 80%, or at least 90%, or at least 95%sequence identity to a polypeptide listed in Table 5, or the SequenceListing; and (l) a nucleotide sequence that encodes a conserved domainof a polypeptide having at least 85%, or at least 90%, or at least 95%,or at least 98% sequence identity to a conserved domain of a polypeptidelisted in Table 4 5, or the Sequence Listing. The recombinantpolynucleotide may further comprise a constitutive, inducible, ortissue-specific promoter operably linked to the nucleotide sequence. Theinvention also relates to compositions comprising at least two of theabove-described polynucleotides.

In a second aspect, the invention comprises an isolated or recombinantpolypeptide comprising a subsequence of at least about 10, or at leastabout 15, or at least about 20, or at least about 30 contiguous aminoacids encoded by the recombinant or isolated polynucleotide describedabove, or comprising a subsequence of at least about 8, or at leastabout 12, or at least about 15, or at least about 20, or at least about30 contiguous amino acids outside a conserved domain.

In a third aspect, the invention comprises an isolated or recombinantpolynucleotide that encodes a polypeptide that is a paralog of theisolated polypeptide described above. In one aspect, the invention is anparalog which, when expressed in Arabidopsis, modifies a trait of theArabidopsis plant.

In a fourth aspect, the invention comprises an isolated or recombinantpolynucleotide that encodes a polypeptide that is an ortholog of theisolated polypeptide described above. In one aspect, the invention is anortholog which, when expressed in Arabidopsis, modifies a trait of theArabidopsis plant.

In a fifth aspect, the invention comprises an isolated polypeptide thatis a paralog of the isolated polypeptide described above. In one aspect,the invention is an paralog which, when expressed in Arabidopsis,modifies a trait of the Arabidopsis plant.

In a sixth aspect, the invention comprises an isolated polypeptide thatis an ortholog of the isolated polypeptide described above. In oneaspect, the invention is an ortholog which, when expressed inArabidopsis, modifies a trait of the Arabidopsis plant.

The present invention also encompasses transcription factor variants. Apreferred transcription factor variant is one having at least 40% aminoacid sequence identity, a more preferred transcription factor variant isone having at least 50% amino acid sequence identity and a mostpreferred transcription factor variant is one having at least 65% aminoacid sequence identity to the transcription factor amino acid sequenceSEQ ID NOs:2 to 2N, where N=2-561, and which contains at least onefunctional or structural characteristic of the transcription factoramino acid sequence. Sequences having lesser degrees of identity butcomparable biological activity are considered to be equivalents.

In another aspect, the invention is a transgenic plant comprising one ormore of the above-described isolated or recombinant polynucleotides. Inyet another aspect, the invention is a plant with altered expressionlevels of a polynucleotide described above or a plant with alteredexpression or activity levels of an above-described polypeptide.Further, the invention is a plant lacking a nucleotide sequence encodinga polypeptide described above or substantially lacking a polypeptidedescribed above. The plant may be any plant, including, but not limitedto, Arabidopsis, mustard, soybean, wheat, corn, potato, cotton, rice,oilseed rape, sunflower, alfalfa, sugarcane, turf, banana, blackberry,blueberry, strawberry, raspberry, cantaloupe, carrot, cauliflower,coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon,onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweetcorn, tobacco, tomato, watermelon, rosaceous fruits, vegetablebrassicas, and mint or other labiates. In yet another aspect, theinventions is an isolated plant material of a plant, including, but notlimited to, plant tissue, fruit, seed, plant cell, embryo, protoplast,pollen, and the like. In yet another aspect, the invention is atransgenic plant tissue culture of regenerable cells, including, but notlimited to, embryos, meristematic cells, microspores, protoplast,pollen, and the like.

In yet another aspect the invention is a transgenic plant comprising oneor more of the above described polynucleotides wherein the encodedpolypeptide is expressed and regulates transcription of a gene.

In a further aspect the invention provides a method of using thepolynucleotide composition to breed a progeny plant from a transgenicplant including crossing plants, producing seeds from transgenic plants,and methods of breeding using transgenic plants, the method comprisingtransforming a plant with the polynucleotide composition to create atransgenic plant, crossing the transgenic plant with another plant,selecting seed, and growing the progeny plant from the seed.

In a further aspect, the invention provides a progeny plant derived froma parental plant wherein said progeny plant exhibits at least three foldgreater messenger RNA levels than said parental plant, wherein themessenger RNA encodes a DNA-binding protein which is capable of bindingto a DNA regulatory sequence and inducing expression of a plant traitgene, wherein the progeny plant is characterized by a change in theplant trait compared to said parental plant. In yet a further aspect,the progeny plant exhibits at least ten fold greater messenger RNAlevels compared to said parental plant. In yet a further aspect, theprogeny plant exhibits at least fifty fold greater messenger RNA levelscompared to said parental plant.

In a further aspect, the invention relates to a cloning or expressionvector comprising the isolated or recombinant polynucleotide describedabove or cells comprising the cloning or expression vector.

In yet a further aspect, the invention relates to a composition producedby incubating a polynucleotide of the invention with a nuclease, arestriction enzyme, a polymerase; a polymerase and a primer; a cloningvector, or with a cell.

Furthermore, the invention relates to a method for producing a planthaving a modified trait. The method comprises altering the expression ofan isolated or recombinant polynucleotide of the invention or alteringthe expression or activity of a polypeptide of the invention in a plantto produce a modified plant, and selecting the modified plant for amodified trait. In one aspect, the plant is a monocot plant. In anotheraspect, the plant is a dicot plant. In another aspect the recombinantpolynucleotide is from a dicot plant and the plant is a monocot plant.In yet another aspect the recombinant polynucleotide is from a monocotplant and the plant is a dicot plant. In yet another aspect therecombinant polynucleotide is from a monocot plant and the plant is amonocot plant. In yet another aspect the recombinant polynucleotide isfrom a dicot plant and the plant is a dicot plant.

In another aspect, the invention is a transgenic plant comprising anisolated or recombinant polynucleotide encoding a polypeptide whereinthe polypeptide is selected from the group consisting of SEQ ID NOs:2-2N, where N=2-561. In yet another aspect, the invention is a plantwith altered expression levels of a polypeptide described above or aplant with altered expression or activity levels of an above-describedpolypeptide. Further, the invention is a plant lacking a polynucleotidesequence encoding a polypeptide described above or substantially lackinga polypeptide described above. The plant may be any plant, including,but not limited to, Arabidopsis, mustard, soybean, wheat, corn, potato,cotton, rice, oilseed rape, sunflower, alfalfa, sugarcane, turf, banana,blackberry, blueberry, strawberry, raspberry, cantaloupe, carrot,cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce,mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach,squash, sweet corn, tobacco, tomato, watermelon, rosaceous fruits,vegetable brassicas, and mint or other labiates. In yet another aspect,the inventions is an isolated plant material of a plant, including, butnot limited to, plant tissue, fruit, seed, plant cell, embryo,protoplast, pollen, and the like. In yet another aspect, the inventionis a transgenic plant tissue culture of regenerable cells, including,but not limited to, embryos, meristematic cells, microspores,protoplast, pollen, and the like.

In another aspect, the invention relates to a method of identifying afactor that is modulated by or interacts with a polypeptide encoded by apolynucleotide of the invention. The method comprises expressing apolypeptide encoded by the polynucleotide in a plant; and identifying atleast one factor that is modulated by or interacts with the polypeptide.In one embodiment the method for identifying modulating or interactingfactors is by detecting binding by the polypeptide to a promotersequence, or by detecting interactions between an additional protein andthe polypeptide in a yeast two hybrid system, or by detecting expressionof a factor by hybridization to a microarray, subtractive hybridization,or differential display.

In yet another aspect, the invention is a method of identifying amolecule that modulates activity or expression of a polynucleotide orpolypeptide of interest. The method comprises placing the molecule incontact with a plant comprising the polynucleotide or polypeptideencoded by the polynucleotide of the invention and monitoring one ormore of the expression level of the polynucleotide in the plant, theexpression level of the polypeptide in the plant, and modulation of anactivity of the polypeptide in the plant.

In yet another aspect, the invention relates to an integrated system,computer or computer readable medium comprising one or more characterstrings corresponding to a polynucleotide of the invention, or to apolypeptide encoded by the polynucleotide. The integrated system,computer or computer readable medium may comprise a link between one ormore sequence strings to a modified plant trait.

In yet another aspect, the invention is a method for identifying asequence similar or homologous to one or more polynucleotides of theinvention, or one or more polypeptides encoded by the polynucleotides.The method comprises providing a sequence database, and querying thesequence database with one or more target sequences corresponding to theone or more polynucleotides or to the one or more polypeptides toidentify one or more sequence members of the database that displaysequence similarity or homology to one or more of the one or more targetsequences.

The method may further comprise of linking the one or more of thepolynucleotides of the invention, or encoded polypeptides, to a modifiedplant phenotype.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING, AND FIGURE

The Sequence Listing provides exemplary polynucleotide and polypeptidesequences of the invention. The traits associated with the use of thesequences are included in the Examples.

CD-ROM1 (Copy 1) is a read-only memory computer-readable compact discand contains a copy of the Sequence Listing in ASCII text format. TheSequence Listing is named “Seq Listing.txt” and is 923 kilobytes insize. The copies of the Sequence Listing on the CD-ROM disc are herebyincorporated by reference in their entirety.

CD-ROM2 (Copy 2) is an exact copy of CD-R1 (Copy 1).

CD-ROM3 contains a CRF copy of the Sequence Listing as a text (.txt)file and is 1846 kilobytes in size.

FIG. 1 shows a phylogenic tree of related plant families adapted fromDaly et al. (2001 Plant Physiology 127:1328-1333).

DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS

In an important aspect, the present invention relates to polynucleotidesand polypeptides, e.g. for modifying phenotypes of plants. Throughoutthis disclosure, various information sources are referred to and/or arespecifically incorporated. The information sources include scientificjournal articles, patent documents, textbooks, and World Wide Webbrowser-inactive page addresses, for example. While the reference tothese information sources clearly indicates that they can be used by oneof skill in the art, applicants specifically incorporate each and everyone of the information sources cited herein, in their entirety, whetheror not a specific mention of “incorporation by reference” is noted. Thecontents and teachings of each and every one of the information sourcescan be relied on and used to make and use embodiments of the invention.

It must be noted that as used herein and in the appended claims, thesingular forms “a,” “an,” and “the” include plural reference unless thecontext clearly dictates otherwise. Thus, for example, a reference to “aplant” includes a plurality of such plants, and a reference to “astress” is a reference to one or more stresses and equivalents thereofknown to those skilled in the art, and so forth.

The polynucleotide sequences of the invention encode polypeptides thatare members of well-known transcription factor families, including planttranscription factor families, as disclosed in Table 5. Generally, thetranscription factors encoded by the present sequences are involved incell differentiation and proliferation and the regulation of growth.Accordingly, one skilled in the art would recognize that by expressingthe present sequences in a plant, one may change the expression ofautologous genes or induce the expression of introduced genes. Byaffecting the expression of similar autologous sequences in a plant thathave the biological activity of the present sequences, or by introducingthe present sequences into a plant, one may alter a plant's phenotype toone with improved traits. The sequences of the invention may also beused to transform a plant and introduce desirable traits not found inthe wild-type cultivar or strain. Plants may then be selected for thosethat produce the most desirable degree of over- or underexpression oftarget genes of interest and coincident trait improvement.

The sequences of the present invention may be from any species,particularly plant species, in a naturally occurring form or from anysource whether natural, synthetic, semi-synthetic or recombinant. Thesequences of the invention may also include fragments of the presentamino acid sequences. In this context, a “fragment” refers to a fragmentof a polypeptide sequence which is at least 5 to about 15 amino acids inlength, most preferably at least 14 amino acids, and which retain somebiological activity of a transcription factor. Where “amino acidsequence” is recited to refer to an amino acid sequence of a naturallyoccurring protein molecule, “amino acid sequence” and like terms are notmeant to limit the amino acid sequence to the complete native amino acidsequence associated with the recited protein molecule.

As one of ordinary skill in the art recognizes, transcription factorscan be identified by the presence of a region or domain of structuralsimilarity or identity to a specific consensus sequence or the presenceof a specific consensus DNA-binding site or DNA-binding site motif (see,for example, Riechmann et al., (2000) Science 290: 2105-2110). The planttranscription factors may belong to one of the following transcriptionfactor families: the AP2 (APETALA2) domain transcription factor family(Riechmann and Meyerowitz (1998) Biol. Chem. 379:633-646); the MYBtranscription factor family (Martin and Paz-Ares, (1997) Trends Genet.13:67-73); the MADS domain transcription factor family (Riechmann andMeyerowitz (1997) Biol. Chem. 378:1079-1101); the WRKY protein family(Ishiguro and Nakamura (1994) Mol. Gen. Genet. 244:563-571); theankyrin-repeat protein family (Zhang et al. (1992) Plant Cell4:1575-1588); the zinc finger protein (Z) family (Klug and Schwabe(1995) FASEB J. 9: 597-604); the homeobox (HB) protein family (Buerglinin Guidebook to the Homeobox Genes, Duboule (ed.) (1994) OxfordUniversity Press); the CAAT-element binding proteins (Forsburg andGuarente (1989) Genes Dev. 3:1166-1178); the squamosa promoter bindingproteins (SPB) (Klein et al. (1996) Mol. Gen. Genet. 1996 250:7-16); theNAM protein family (Souer et al. (1996) Cell 85:159-170); the IAA/AUXproteins (Rouse et al. (1998) Science 279:1371-1373); the HLH/MYCprotein family (Littlewood et al. (1994) Prot. Profile 1:639-709); theDNA-binding protein (DBP) family (Tucker et al. (1994) EMBO J.13:2994-3002); the bZIP family of transcription factors (Foster et al.(1994) FASEB J. 8:192-200); the Box P-binding protein (the BPF-1) family(da Costa e Silva et al. (1993) Plant J 4:125-135); the high mobilitygroup (HMG) family (Bustin and Reeves (1996) Prog. Nucl. Acids Res. Mol.Biol. 54:35-100); the scarecrow (SCR) family (Di Laurenzio et al. (1996)Cell 86:423-433); the GF14 family (Wu et al. (1997) Plant Physiol.114:1421-1431); the polycomb (PCOMB) family (Kennison (1995) Annu. Rev.Genet. 29:289-303); the teosinte branched (TEO) family (Luo et al.(1996) Nature 383:794-799; the ABI3 family (Giraudat et al. (1992) PlantCell 4:1251-1261); the triple helix (TH) family (Dehesh et al. (1990)Science 250:1397-1399); the EIL family (Chao et al. (1997) Cell89:1133-44); the AT-HOOK family (Reeves and Nissen (1990) J. Biol. Chem.265:8573-8582); the S1FA family (Zhou et al. (1995) Nucleic Acids Res.23:1165-1169); the bZIPT2 family (Lu and Ferl (1995) Plant Physiol.109:723); the YABBY family (Bowman et al. (1999) Development126:2387-96); the PAZ family (Bohmert et al. (1998) EMBO J. 17:170-80);a family of miscellaneous (MISC) transcription factors including theDPBF family (Kim et al. (1997) Plant J 11:1237-1251) and the SPF1 family(Ishiguro and Nakamura (1994) Mol. Gen. Genet. 244:563-571); the golden(GLD) family (Hall et al. (1998) Plant Cell 10:925-936), the TUBBYfamily (Boggin et al, (1999) Science 286:2119-2125), the heat shockfamily (Wu C (1995) Annu Rev Cell Dev Biol 11:441-469), the ENBP family(Christiansen et al (1996) Plant Mol Biol 32:809-821), the RING-zincfamily (Jensen et al. (1998) FEBS letters 436:283-287), the PDBP family(Janik et al Virology. (1989) 168:320-329), the PCF family (Cubas P, etal. Plant J. (1999) 18:215-22), the SRS(SHI-related) family (Fridborg etal Plant Cell (1999) 11:1019-1032), the CPP (cysteine-richpolycomb-like) family (Cvitanich et al Proc. Natl. Acad. Sci. USA.(2000) 97:8163-8168), the ARF (auxin response factor) family (Ulmasov,et al. (1999) Proc. Natl. Acad. Sci. USA 96: 5844-5849), the SWI/SNFfamily (Collingwood et al J. Mol. End. 23:255-275), the ACBF family(Seguin et al (1997) Plant Mol. Biol. 35:281-291), PCGL (CG-1 like)family (da Costa e Silva et al. (1994) Plant Mol Biol. 25:921-924) theARID family (Vazquez et al. (1999) Development. 126: 733-42), theJumonji family, Balciunas et al (2000, Trends Biochem Sci. 25: 274-276),the bZIP-NIN family (Schauser et al (1999) Nature 402: 191-195), the E2Ffamily Kaelin et al (1992) Cell 70: 351-364) and the GRF-like family(Knaap et al (2000) Plant Physiol. 122: 695-704). As indicated by anypart of the list above and as known in the art, transcription factorshave been sometimes categorized by class, family, and sub-familyaccording to their structural content and consensus DNA-binding sitemotif, for example. Many of the classes and many of the families andsub-families are listed here. However, the inclusion of one sub-familyand not another, or the inclusion of one family and not another, doesnot mean that the invention does not encompass polynucleotides orpolypeptides of a certain family or sub-family. The list provided hereis merely an example of the types of transcription factors and theknowledge available concerning the consensus sequences and consensusDNA-binding site motifs that help define them as known to those of skillin the art (each of the references noted above are specificallyincorporated herein by reference). A transcription factor may include,but is not limited to, any polypeptide that can activate or represstranscription of a single gene or a number of genes. This polypeptidegroup includes, but is not limited to, DNA-binding proteins, DNA-bindingprotein binding proteins, protein kinases, protein phosphatases,GTP-binding proteins, and receptors, and the like.

In addition to methods for modifying a plant phenotype by employing oneor more polynucleotides and polypeptides of the invention describedherein, the polynucleotides and polypeptides of the invention have avariety of additional uses. These uses include their use in therecombinant production (i.e., expression) of proteins; as regulators ofplant gene expression, as diagnostic probes for the presence ofcomplementary or partially complementary nucleic acids (including fordetection of natural coding nucleic acids); as substrates for furtherreactions, e.g., mutation reactions, PCR reactions, or the like; assubstrates for cloning e.g., including digestion or ligation reactions;and for identifying exogenous or endogenous modulators of thetranscription factors. A “polynucleotide” is a nucleic acid sequencecomprising a plurality of polymerized nucleotides, e.g., at least about15 consecutive polymerized nucleotides, optionally at least about 30consecutive nucleotides, at least about 50 consecutive nucleotides. Inmany instances, a polynucleotide comprises a nucleotide sequenceencoding a polypeptide (or protein) or a domain or fragment thereof.Additionally, the polynucleotide may comprise a promoter, an intron, anenhancer region, a polyadenylation site, a translation initiation site,5′ or 3′ untranslated regions, a reporter gene, a selectable marker, orthe like. The polynucleotide can be single stranded or double strandedDNA or RNA. The polynucleotide optionally comprises modified bases or amodified backbone. The polynucleotide can be, e.g., genomic DNA or RNA,a transcript (such as an mRNA), a cDNA, a PCR product, a cloned DNA, asynthetic DNA or RNA, or the like. The polynucleotide can comprise asequence in either sense or antisense orientations.

A “recombinant polynucleotide” is a polynucleotide that is not in itsnative state, e.g., the polynucleotide comprises a nucleotide sequencenot found in nature, or the polynucleotide is in a context other thanthat in which it is naturally found, e.g., separated from nucleotidesequences with which it typically is in proximity in nature, or adjacent(or contiguous with) nucleotide sequences with which it typically is notin proximity. For example, the sequence at issue can be cloned into avector, or otherwise recombined with one or more additional nucleicacid.

An “isolated polynucleotide” is a polynucleotide whether naturallyoccurring or recombinant, that is present outside the cell in which itis typically found in nature, whether purified or not. Optionally, anisolated polynucleotide is subject to one or more enrichment orpurification procedures, e.g., cell lysis, extraction, centrifugation,precipitation, or the like.

A “polypeptide” is an amino acid sequence comprising a plurality ofconsecutive polymerized amino acid residues e.g., at least about 15consecutive polymerized amino acid residues, optionally at least about30 consecutive polymerized amino acid residues, at least about 50consecutive polymerized amino acid residues. In many instances, apolypeptide comprises a polymerized amino acid residue sequence that isa transcription factor or a domain or portion or fragment thereof.Additionally, the polypeptide may comprise a localization domain, 2) anactivation domain, 3) a repression domain, 4) an oligomerization domainor 5) a DNA-binding domain, or the like. The polypeptide optionallycomprises modified amino acid residues, naturally occurring amino acidresidues not encoded by a codon, non-naturally occurring amino acidresidues.

A “recombinant polypeptide” is a polypeptide produced by translation ofa recombinant polynucleotide. A “synthetic polypeptide” is a polypeptidecreated by consecutive polymerization of isolated amino acid residuesusing methods well known in the art. An “isolated polypeptide,” whethera naturally occurring or a recombinant polypeptide, is more enriched in(or out of) a cell than the polypeptide in its natural state in a wildtype cell, e.g., more than about 5% enriched, more than about 10%enriched, or more than about 20%, or more than about 50%, or more,enriched, i.e., alternatively denoted: 105%, 110%, 120%, 150% or more,enriched relative to wild type standardized at 100%. Such an enrichmentis not the result of a natural response of a wild type plant.Alternatively, or additionally, the isolated polypeptide is separatedfrom other cellular components with which it is typically associated,e.g., by any of the various protein purification methods herein.

“Identity” or “similarity” refers to sequence similarity between twopolynucleotide sequences or between two polypeptide sequences, withidentity being a more strict comparison. The phrases “percent identity”and “% identity” refer to the percentage of sequence similarity found ina comparison of two or more polynucleotide sequences or two or morepolypeptide sequences. Identity or similarity can be determined bycomparing a position in each sequence that may be aligned for purposesof comparison. When a position in the compared sequence is occupied bythe same nucleotide base or amino acid, then the molecules are identicalat that position. A degree of similarity or identity betweenpolynucleotide sequences is a function of the number of identical ormatching nucleotides at positions shared by the polynucleotidesequences. A degree of identity of polypeptide sequences is a functionof the number of identical amino acids at positions shared by thepolypeptide sequences. A degree of homology or similarity of polypeptidesequences is a function of the number of amino acids, i.e., structurallyrelated, at positions shared by the polypeptide sequences.

“Altered” nucleic acid sequences encoding polypeptide include thosesequences with deletions, insertions, or substitutions of differentnucleotides, resulting in a polynucleotide encoding a polypeptide withat least one functional characteristic of the polypeptide. Includedwithin this definition are polymorphisms that may or may not be readilydetectable using a particular oligonucleotide probe of thepolynucleotide encoding polypeptide, and improper or unexpectedhybridization to allelic variants, with a locus other than the normalchromosomal locus for the polynucleotide sequence encoding polypeptide.The encoded polypeptide protein may also be “altered”, and may containdeletions, insertions, or substitutions of amino acid residues thatproduce a silent change and result in a functionally equivalentpolypeptide. Deliberate amino acid substitutions may be made on thebasis of similarity in residue side chain chemistry, including, but notlimited to, polarity, charge, solubility, hydrophobicity,hydrophilicity, and/or the amphipathic nature of the residues, as longas the biological activity of polypeptide is retained. For example,negatively charged amino acids may include aspartic acid and glutamicacid, positively charged amino acids may include lysine and arginine,and amino acids with uncharged polar head groups having similarhydrophilicity values may include leucine, isoleucine, and valine;glycine and alanine; asparagine and glutamine; serine and threonine; andphenylalanine and tyrosine. Alignments between different polypeptidesequences may be used to calculate “percentage sequence similarity”.

The term “plant” includes whole plants, shoot vegetativeorgans/structures (e.g., leaves, stems and tubers), roots, flowers andfloral organs/structures (e.g., bracts, sepals, petals, stamens,carpels, anthers and ovules), seed (including embryo, endosperm, andseed coat) and fruit (the mature ovary), plant tissue (e.g., vasculartissue, ground tissue, and the like) and cells (e.g., guard cells, eggcells, and the like), and progeny of same. The class of plants that canbe used in the method of the invention is generally as broad as theclass of higher and lower plants amenable to transformation techniques,including angiosperms (monocotyledonous and dicotyledonous plants),gymnosperms, ferns, horsetails, psilophytes, lycophytes, bryophytes, andmulticellular algae. (See for example, FIG. 1, adapted from Daly et al.2001 Plant Physiology 127:1328-1333; and see also Tudge, C., The Varietyof Life, Oxford University Press, New York, 2000, pp. 547-606.)

A “transgenic plant” refers to a plant that contains genetic materialnot found in a wild type plant of the same species, variety or cultivar.The genetic material may include a transgene, an insertional mutagenesisevent (such as by transposon or T-DNA insertional mutagenesis), anactivation tagging sequence, a mutated sequence, a homologousrecombination event or a sequence modified by chimeraplasty. Typically,the foreign genetic material has been introduced into the plant by humanmanipulation, but any method can be used as one of skill in the artrecognizes.

A transgenic plant may contain an expression vector or cassette. Theexpression cassette typically comprises a polypeptide-encoding sequenceoperably linked (i.e., under regulatory control of) to appropriateinducible or constitutive regulatory sequences that allow for theexpression of polypeptide. The expression cassette can be introducedinto a plant by transformation or by breeding after transformation of aparent plant. A plant refers to a whole plant as well as to a plantpart, such as seed, fruit, leaf, or root, plant tissue, plant cells orany other plant material, e.g., a plant explant, as well as to progenythereof, and to in vitro systems that mimic biochemical or cellularcomponents or processes in a cell.

“Ectopic expression or altered expression” in reference to apolynucleotide indicates that the pattern of expression in, e.g., atransgenic plant or plant tissue, is different from the expressionpattern in a wild type plant or a reference plant of the same species.The pattern of expression may also be compared with a referenceexpression pattern in a wild type plant of the same species. Forexample, the polynucleotide or polypeptide is expressed in a cell ortissue type other than a cell or tissue type in which the sequence isexpressed in the wild type plant, or by expression at a time other thanat the time the sequence is expressed in the wild type plant, or by aresponse to different inducible agents, such as hormones orenvironmental signals, or at different expression levels (either higheror lower) compared with those found in a wild type plant. The term alsorefers to altered expression patterns that are produced by lowering thelevels of expression to below the detection level or completelyabolishing expression. The resulting expression pattern can be transientor stable, constitutive or inducible. In reference to a polypeptide, theterm “ectopic expression or altered expression” further may relate toaltered activity levels resulting from the interactions of thepolypeptides with exogenous or endogenous modulators or frominteractions with factors or as a result of the chemical modification ofthe polypeptides.

A “fragment” or “domain,” with respect to a polypeptide, refers to asubsequence of the polypeptide. In some cases, the fragment or domain,is a subsequence of the polypeptide which performs at least onebiological function of the intact polypeptide in substantially the samemanner, or to a similar extent, as does the intact polypeptide. Forexample, a polypeptide fragment can comprise a recognizable structuralmotif or functional domain such as a DNA-binding site or domain thatbinds to a DNA promoter region, an activation domain, or a domain forprotein-protein interactions. Fragments can vary in size from as few as6 amino acids to the full length of the intact polypeptide, but arepreferably at least about 30 amino acids in length and more preferablyat least about 60 amino acids in length. In reference to apolynucleotide sequence, “a fragment” refers to any subsequence of apolynucleotide, typically, of at least about 15 consecutive nucleotides,preferably at least about 30 nucleotides, more preferably at least about50 nucleotides, of any of the sequences provided herein.

The invention also encompasses production of DNA sequences that encodetranscription factors and transcription factor derivatives, or fragmentsthereof, entirely by synthetic chemistry. After production, thesynthetic sequence may be inserted into any of the many availableexpression vectors and cell systems using reagents well known in theart. Moreover, synthetic chemistry may be used to introduce mutationsinto a sequence encoding transcription factors or any fragment thereof.

A “conserved domain”, with respect to a polypeptide, refers to a domainwithin a transcription factor family which exhibits a higher degree ofsequence homology, such as at least 65% sequence identity includingconservative substitutions, and preferably at least 80% sequenceidentity, and more preferably at least 85%, or at least about 86%, or atleast about 87%, or at least about 88%, or at least about 90%, or atleast about 95%, or at least about 98% amino acid residue sequenceidentity of a polypeptide of consecutive amino acid residues. A fragmentor domain can be referred to as outside a consensus sequence or outsidea consensus DNA-binding site that is known to exist or that exists for aparticular transcription factor class, family, or sub-family. In thiscase, the fragment or domain will not include the exact amino acids of aconsensus sequence or consensus DNA-binding site of a transcriptionfactor class, family or sub-family, or the exact amino acids of aparticular transcription factor consensus sequence or consensusDNA-binding site. Furthermore, a particular fragment, region, or domainof a polypeptide, or a polynucleotide encoding a polypeptide, can be“outside a conserved domain” if all the amino acids of the fragment,region, or domain fall outside of a defined conserved domain(s) for apolypeptide or protein. The conserved domains for each of polypeptidesof SEQ ID NOs:2-2N, where N=2-561, are listed in Table 5 as described inExample VII. Also, many of the polypeptides of Table 5 have conserveddomains specifically indicated by start and stop sites. A comparison ofthe regions of the polypeptides in SEQ ID NOs:2-2N, where N=2-561, or ofthose in Table 5, allows one of skill in the art to identify conserveddomain(s) for any of the polypeptides listed or referred to in thisdisclosure, including those in Table 5.

A “trait” refers to a physiological, morphological, biochemical, orphysical characteristic of a plant or particular plant material or cell.In some instances, this characteristic is visible to the human eye, suchas seed or plant size, or can be measured by biochemical techniques,such as detecting the protein, starch, or oil content of seed or leaves,or by observation of a metabolic or physiological process, e.g. bymeasuring uptake of carbon dioxide, or by the observation of theexpression level of a gene or genes, e.g., by employing Northernanalysis, RT-PCR, microarray gene expression assays, or reporter geneexpression systems, or by agricultural observations such as stresstolerance, yield, or pathogen tolerance. Any technique can be used tomeasure the amount of, comparative level of, or difference in anyselected chemical compound or macromolecule in the transgenic plants,however.

“Trait modification” refers to a detectable difference in acharacteristic in a plant ectopically expressing a polynucleotide orpolypeptide of the present invention relative to a plant not doing so,such as a wild type plant. In some cases, the trait modification can beevaluated quantitatively. For example, the trait modification can entailat least about a 2% increase or decrease in an observed trait(difference), at least a 5% difference, at least about a 10% difference,at least about a 20% difference, at least about a 30%, at least about a50%, at least about a 70%, or at least about a 100%, or an even greaterdifference compared with a wild type plant. It is known that there canbe a natural variation in the modified trait. Therefore, the traitmodification observed entails a change of the normal distribution of thetrait in the plants compared with the distribution observed in wild typeplant.

I. TRAITS WHICH MAY BE MODIFIED

Trait modifications of particular interest include those to seed (suchas embryo or endosperm), fruit, root, flower, leaf, stem, shoot,seedling or the like, including: enhanced tolerance to environmentalconditions including freezing, chilling, heat, drought, watersaturation, radiation and ozone; improved tolerance to microbial, fungalor viral diseases; improved tolerance to pest infestations, includingnematodes, mollicutes, parasitic higher plants or the like; decreasedherbicide sensitivity; improved tolerance of heavy metals or enhancedability to take up heavy metals; improved growth under poorphotoconditions (e.g., low light and/or short day length), or changes inexpression levels of genes of interest. Other phenotype that can bemodified relate to the production of plant metabolites, such asvariations in the production of taxol, tocopherol, tocotrienol, sterols,phytosterols, vitamins, wax monomers, anti-oxidants, amino acids,lignins, cellulose, tannins, prenyllipids (such as chlorophylls andcarotenoids), glucosinolates, and terpenoids, enhanced orcompositionally altered protein or oil production (especially in seeds),or modified sugar (insoluble or soluble) and/or starch composition.Physical plant characteristics that can be modified include celldevelopment (such as the number of trichomes), fruit and seed size andnumber, yields of plant parts such as stems, leaves, inflorescences, androots, the stability of the seeds during storage, characteristics of theseed pod (e.g., susceptibility to shattering), root hair length andquantity, internode distances, or the quality of seed coat. Plant growthcharacteristics that can be modified include growth rate, germinationrate of seeds, vigor of plants and seedlings, leaf and flowersenescence, male sterility, apomixis, flowering time, flower abscission,rate of nitrogen uptake, osmotic sensitivity to soluble sugarconcentrations, biomass or transpiration characteristics, as well asplant architecture characteristics such as apical dominance, branchingpatterns, number of organs, organ identity, organ shape or size.

Transcription Factors Modify Expression of Endogenous Genes

Expression of genes which encode transcription factors that modifyexpression of endogenous genes, polynucleotides, and proteins are wellknown in the art. In addition, transgenic plants comprising isolatedpolynucleotides encoding transcription factors may also modifyexpression of endogenous genes, polynucleotides, and proteins. Examplesinclude Peng et al. (1997, Genes and Development 11:3194-3205) and Penget al. (1999, Nature, 400:256-261). In addition, many others havedemonstrated that an Arabidopsis transcription factor expressed in anexogenous plant species elicits the same or very similar phenotypicresponse. See, for example, Fu et al. (2001, Plant Cell 13:1791-1802);Nandi et al. (2000, Curr. Biol. 10:215-218); Coupland (1995, Nature377:482-483); and Weigel and Nilsson (1995, Nature 377:482-500).

In another example, Mandel et al. (1992, Cell 71-133-143) and Suzuki etal. (2001, Plant J. 28:409-418) teach that a transcription factorexpressed in another plant species elicits the same or very similarphenotypic response of the endogenous sequence, as often predicted inearlier studies of Arabidopsis transcription factors in Arabidopsis (seeMandel et al., 1992, supra; Suzuki et al., 2001, supra).

Other examples include Müller et al. (2001, Plant J. 28:169-179); Kim etal. (2001, Plant J. 25:247-259); Kyozuka and Shimamoto (2002, Plant CellPhysiol. 43:130-135); Boss and Thomas (2002, Nature, 416:847-850); He etal. (2000, Transgenic Res., 9:223-227); and Robson et al. (2001, PlantJ. 28:619-631).

In yet another example, Gilmour et al. (1998, Plant J. 16:433-442) teachan Arabidopsis AP2 transcription factor, CBF1, which, when overexpressedin transgenic plants, increases plant freezing tolerance. Jaglo et al(2001, Plant Physiol. 127:910-017) further identified sequences inBrassica napus which encode CBF-like genes and that transcripts forthese genes accumulated rapidly in response to low temperature.Transcripts encoding CBF-like proteins were also found to accumulaterapidly in response to low temperature in wheat, as well as in tomato.An alignment of the CBF proteins from Arabidopsis, B. napus, wheat, rye,and tomato revealed the presence of conserved amino acid sequences,PKK/RPAGRxKFxETRHP and DSAWR, that bracket the AP2/EREBP DNA bindingdomains of the proteins and distinguish them from other members of theAP2/EREBP protein family. (See Jaglo et al., supra.)

III. POLYPEPTIDES AND POLYNUCLEOTIDES OF THE INVENTION

The present invention provides, among other things, transcriptionfactors (TFs), and transcription factor homologue polypeptides, andisolated or recombinant polynucleotides encoding the polypeptides, ornovel variant polypeptides or polynucleotides encoding novel variants oftranscription factors derived from the specific sequences provided here.These polypeptides and polynucleotides may be employed to modify aplant's characteristic. Exemplary polynucleotides encoding thepolypeptides of the invention were identified in the Arabidopsisthaliana GenBank database using publicly available sequence analysisprograms and parameters. Sequences initially identified were thenfurther characterized to identify sequences comprising specifiedsequence strings corresponding to sequence motifs present in families ofknown transcription factors. In addition, further exemplarypolynucleotides encoding the polypeptides of the invention wereidentified in the plant GenBank database using publicly availablesequence analysis programs and parameters. Sequences initiallyidentified were then further characterized to identify sequencescomprising specified sequence strings corresponding to sequence motifspresent in families of known transcription factors. Polynucleotidesequences meeting such criteria were confirmed as transcription factors.

Additional polynucleotides of the invention were identified by screeningArabidopsis thaliana and/or other plant cDNA libraries with probescorresponding to known transcription factors under low stringencyhybridization conditions. Additional sequences, including full lengthcoding sequences were subsequently recovered by the rapid amplificationof cDNA ends (RACE) procedure, using a commercially available kitaccording to the manufacturer's instructions. Where necessary, multiplerounds of RACE are performed to isolate 5′ and 3′ ends. The full lengthcDNA was then recovered by a routine end-to-end polymerase chainreaction (PCR) using primers specific to the isolated 5′ and 3′ ends.Exemplary sequences are provided in the Sequence Listing.

The polynucleotides of the invention can be or were ectopicallyexpressed in overexpressor or knockout plants and the changes in thecharacteristic(s) or trait(s) of the plants observed. Therefore, thepolynucleotides and polypeptides can be employed to improve thecharacteristics of plants.

The polynucleotides of the invention can be or were ectopicallyexpressed in overexpressor plant cells and the changes in the expressionlevels of a number of genes, polynucleotides, and/or proteins of theplant cells observed. Therefore, the polynucleotides and polypeptidescan be employed to change expression levels of a genes, polynucleotides,and/or proteins of plants.

IV. PRODUCING POLYPEPTIDES

The polynucleotides of the invention include sequences that encodetranscription factors and transcription factor homologue polypeptidesand sequences complementary thereto, as well as unique fragments ofcoding sequence, or sequence complementary thereto. Such polynucleotidescan be, e.g., DNA or RNA, e.g., mRNA, cRNA, synthetic RNA, genomic DNA,cDNA synthetic DNA, oligonucleotides, etc. The polynucleotides areeither double-stranded or single-stranded, and include either, or bothsense (i.e., coding) sequences and antisense (i.e., non-coding,complementary) sequences. The polynucleotides include the codingsequence of a transcription factor, or transcription factor homologuepolypeptide, in isolation, in combination with additional codingsequences (e.g., a purification tag, a localization signal, as afusion-protein, as a pre-protein, or the like), in combination withnon-coding sequences (e.g., introns or inteins, regulatory elements suchas promoters, enhancers, terminators, and the like), and/or in a vectoror host environment in which the polynucleotide encoding a transcriptionfactor or transcription factor homologue polypeptide is an endogenous orexogenous gene.

A variety of methods exist for producing the polynucleotides of theinvention. Procedures for identifying and isolating DNA clones are wellknown to those of skill in the art, and are described in, e.g., Bergerand Kimmel, Guide to Molecular Cloning Techniques Methods in Enzymologyvolume 152 Academic Press, Inc., San Diego, Calif. (“Berger”); Sambrooket al., Molecular Cloning—A Laboratory Manual (2nd Ed.), Vol. 1-3, ColdSpring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989 (“Sambrook”)and Current Protocols in Molecular Biology, F. M. Ausubel et al., eds.,Current Protocols, a joint venture between Greene Publishing Associates,Inc. and John Wiley & Sons, Inc., (supplemented through 2000)(“Ausubel”).

Alternatively, polynucleotides of the invention, can be produced by avariety of in vitro amplification methods adapted to the presentinvention by appropriate selection of specific or degenerate primers.Examples of protocols sufficient to direct persons of skill through invitro amplification methods, including the polymerase chain reaction(PCR) the ligase chain reaction (LCR), Qbeta-replicase amplification andother RNA polymerase mediated techniques (e.g., NASBA), e.g., for theproduction of the homologous nucleic acids of the invention are found inBerger (supra), Sambrook (supra), and Ausubel (supra), as well as Mulliset al., (1987) PCR Protocols A Guide to Methods and Applications (Inniset al. eds) Academic Press Inc. San Diego, Calif. (1990) (Innis).Improved methods for cloning in vitro amplified nucleic acids aredescribed in Wallace et al., U.S. Pat. No. 5,426,039. Improved methodsfor amplifying large nucleic acids by PCR are summarized in Cheng et al.(1994) Nature 369: 684-685 and the references cited therein, in whichPCR amplicons of up to 40 kb are generated. One of skill will appreciatethat essentially any RNA can be converted into a double stranded DNAsuitable for restriction digestion, PCR expansion and sequencing usingreverse transcriptase and a polymerase. See, e.g., Ausubel, Sambrook andBerger, all supra.

Alternatively, polynucleotides and oligonucleotides of the invention canbe assembled from fragments produced by solid-phase synthesis methods.Typically, fragments of up to approximately 100 bases are individuallysynthesized and then enzymatically or chemically ligated to produce adesired sequence, e.g., a polynucleotide encoding all or part of atranscription factor. For example, chemical synthesis using thephosphoramidite method is described, e.g., by Beaucage et al. (1981)Tetrahedron Letters 22:1859-1869; and Matthes et al. (1984) EMBO J.3:801-805. According to such methods, oligonucleotides are synthesized,purified, annealed to their complementary strand, ligated and thenoptionally cloned into suitable vectors. And if so desired, thepolynucleotides and polypeptides of the invention can be custom orderedfrom any of a number of commercial suppliers.

V. HOMOLOGOUS SEQUENCES

Sequences homologous, i.e., that share significant sequence identity orsimilarity, to those provided in the Sequence Listing, derived fromArabidopsis thaliana or from other plants of choice are also an aspectof the invention. Homologous sequences can be derived from any plantincluding monocots and dicots and in particular agriculturally importantplant species, including but not limited to, crops such as soybean,wheat, corn, potato, cotton, rice, rape, oilseed rape (includingcanola), sunflower, alfalfa, sugarcane and turf; or fruits andvegetables, such as banana, blackberry, blueberry, strawberry, andraspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant,grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers,pineapple, pumpkin, spinach, squash, sweet corn, tobacco, tomato,watermelon, rosaceous fruits (such as apple, peach, pear, cherry andplum) and vegetable brassicas (such as broccoli, cabbage, cauliflower,Brussels sprouts, and kohlrabi). Other crops, fruits and vegetableswhose phenotype can be changed include barley, rye, millet, sorghum,currant, avocado, citrus fruits such as oranges, lemons, grapefruit andtangerines, artichoke, cherries, nuts such as the walnut and peanut,endive, leek, roots, such as arrowroot, beet, cassaya, turnip, radish,yam, and sweet potato, and beans. The homologous sequences may also bederived from woody species, such pine, poplar and eucalyptus, or mint orother labiates.

Orthologs And Paralogs

Several different methods are known by those of skill in the art foridentifying and defining these functionally homologous sequences. Threegeneral methods for defining paralogs and orthologs are described; aparalog or ortholog or homolog may be identified by one or more of themethods described below.

Orthologs and paralogs are evolutionarily related genes that havesimilar sequence and similar functions. Orthologs are structurallyrelated genes in different species that are derived from a speciationevent. Paralogs are structurally related genes within a single speciesthat are derived by a duplication event.

Within a single plant species, gene duplication may cause two copies ofa particular gene, giving rise to two or more genes with similarsequence and similar function known as paralogs. A paralog is thereforea similar gene with a similar function within the same species. Paralogstypically cluster together or in the same lade (a group of similargenes) when a gene family phylogeny is analyzed using programs such asCLUSTAL (Thompson et al. (1994) Nucleic Acids Res. 22:4673-4680; Higginset al. (1996) Methods Enzymol. 266 383-402). Groups of similar genes canalso be identified with pair-wise BLAST analysis (Feng and Doolittle(1987) J. Mol. Evol. 25:351-360). For example, a lade of very similarMADS domain transcription factors from Arabidopsis all share a commonfunction in flowering time (Ratcliffe et al. (2001) Plant Physiol.126:122-132), and a group of very similar AP2 domain transcriptionfactors from Arabidopsis are involved in tolerance of plants to freezing(Gilmour et al. (1998) Plant J. 16:433-442). Analysis of groups ofsimilar genes with similar function that fall within one clade can yieldsub-sequences that are particular to the clade. These sub-sequences,known as consensus sequences, can not only be used to define thesequences within each clade, but define the functions of these genes;genes within a clade may contain paralogous or orthologous sequencesthat share the same function. (See also, for example, Mount, D. W.(2001) Bioinformatics: Sequence and Genome Analysis Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. page 543.)

Speciation, the production of new species from a parental species, canalso give rise to two or more genes with similar sequence and similarfunction. These genes, termed orthologs, often have an identicalfunction within their host plants and are often interchangeable betweenspecies without losing function. Because plants have common ancestors,many genes in any plant species will have a corresponding orthologousgene in another plant species. Once a phylogenic tree for a gene familyof one species has been constructed using a program such as CLUSTAL(Thompson et al. (1994) Nucleic Acids Res. 22:4673-4680; Higgins et al.(1996) Methods Enzymol. 266:383-402), potential orthologous sequencescan placed into the phylogenetic tree and its relationship to genes fromthe species of interest can be determined. Once the ortholog pair hasbeen identified, the function of the test ortholog can be determined bydetermining the function of the reference ortholog.

Transcription factors that are homologous to the listed sequences willtypically share at least about 30% amino acid sequence identity, or atleast about 30% amino acid sequence identity outside of a knownconsensus sequence or consensus DNA-binding site. More closely relatedtranscription factors can share at least about 50%, about 60%, about65%, about 70%, about 75% or about 80% or about 90% or about 95% orabout 98% or more sequence identity with the listed sequences, or withthe listed sequences but excluding or outside a known consensus sequenceor consensus DNA-binding site, or with the listed sequences excludingone or all conserved domain. Factors that are most closely related tothe listed sequences share, e.g., at least about 85%, about 90% or about95% or more % sequence identity to the listed sequences, or to thelisted sequences but excluding or outside a known consensus sequence orconsensus DNA-binding site or outside one or all conserved domain. Atthe nucleotide level, the sequences will typically share at least about40% nucleotide sequence identity, preferably at least about 50%, about60%, about 70% or about 80% sequence identity, and more preferably about85%, about 90%, about 95% or about 97% or more sequence identity to oneor more of the listed sequences, or to a listed sequence but excludingor outside a known consensus sequence or consensus DNA-binding site, oroutside one or all conserved domain. The degeneracy of the genetic codeenables major variations in the nucleotide sequence of a polynucleotidewhile maintaining the amino acid sequence of the encoded protein.Conserved domains within a transcription factor family may exhibit ahigher degree of sequence homology, such as at least 65% sequenceidentity including conservative substitutions, and preferably at least80% sequence identity, and more preferably at least 85%, or at leastabout 86%, or at least about 87%, or at least about 88%, or at leastabout 90%, or at least about 95%, or at least about 98% sequenceidentity. Transcription factors that are homologous to the listedsequences should share at least 30%, or at least about 60%, or at leastabout 75%, or at least about 80%, or at least about 90%, or at leastabout 95% amino acid sequence identity over the entire length of thepolypeptide or the homolog. In addition, transcription factors that arehomologous to the listed sequences should share at least 30%, or atleast about 60%, or at least about 75%, or at least about 80%, or atleast about 90%, or at least about 95% amino acid sequence similarityover the entire length of the polypeptide or the homolog.

Percent identity can be determined electronically, e.g., by using theMEGALIGN program (DNASTAR, Inc. Madison, Wis.). The MEGALIGN program cancreate alignments between two or more sequences according to differentmethods, e.g., the clustal method. (See, e.g., Higgins, D. G. and P. M.Sharp (1988) Gene 73:237-244.) The clustal algorithm groups sequencesinto clusters by examining the distances between all pairs. The clustersare aligned pairwise and then in groups. Other alignment algorithms orprograms may be used, including FASTA, BLAST, or ENTREZ, FASTA andBLAST. These are available as a part of the GCG sequence analysispackage (University of Wisconsin, Madison, Wis.), and can be used withor without default settings. ENTREZ is available through the NationalCenter for Biotechnology Information. In one embodiment, the percentidentity of two sequences can be determined by the GCG program with agap weight of 1, e.g., each amino acid gap is weighted as if it were asingle amino acid or nucleotide mismatch between the two sequences (seeU.S. Pat. No. 6,262,333).

Other techniques for alignment are described in Methods in Enzymology,vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996),ed. Doolittle, Academic Press, Inc., San Diego, Calif., USA. Preferably,an alignment program that permits gaps in the sequence is utilized toalign the sequences. The Smith-Waterman is one type of algorithm thatpermits gaps in sequence alignments. See Methods Mol. Biol. 70: 173-187(1997). Also, the GAP program using the Needleman and Wunsch alignmentmethod can be utilized to align sequences. An alternative searchstrategy uses MPSRCH software, which runs on a MASPAR computer. MPSRCHuses a Smith-Waterman algorithm to score sequences on a massivelyparallel computer. This approach improves ability to pick up distantlyrelated matches, and is especially tolerant of small gaps and nucleotidesequence errors. Nucleic acid-encoded amino acid sequences can be usedto search both protein and DNA databases.

The percentage similarity between two polypeptide sequences, e.g.,sequence A and sequence B, is calculated by dividing the length ofsequence A, minus the number of gap residues in sequence A, minus thenumber of gap residues in sequence B, into the sum of the residuematches between sequence A and sequence B, times one hundred. Gaps oflow or of no similarity between the two amino acid sequences are notincluded in determining percentage similarity. Percent identity betweenpolynucleotide sequences can also be counted or calculated by othermethods known in the art, e.g., the Jotun Hein method. (See, e.g., Hein,J. (1990) Methods Enzymol. 183:626-645.) Identity between sequences canalso be determined by other methods known in the art, e.g., by varyinghybridization conditions (see US Patent Application No. 20010010913).

Thus, the invention provides methods for identifying a sequence similaror paralogous or orthologous or homologous to one or morepolynucleotides as noted herein, or one or more target polypeptidesencoded by the polynucleotides, or otherwise noted herein and mayinclude linking or associating a given plant phenotype or gene functionwith a sequence. In the methods, a sequence database is provided(locally or across an inter or intra net) and a query is made againstthe sequence database using the relevant sequences herein and associatedplant phenotypes or gene functions.

In addition, one or more polynucleotide sequences or one or morepolypeptides encoded by the polynucleotide sequences may be used tosearch against a BLOCKS (Bairoch et al. (1997) Nucleic Acids Res.25:217-221), PFAM, and other databases which contain previouslyidentified and annotated motifs, sequences and gene functions. Methodsthat search for primary sequence patterns with secondary structure gappenalties (Smith et al. (1992) Protein Engineering 5:35-51) as well asalgorithms such as Basic Local Alignment Search Tool (BLAST; Altschul,S. F. (1993) J. Mol. Evol. 36:290-300; Altschul et al. (1990) supra),BLOCKS (Henikoff, S, and Henikoff, G. J. (1991) Nucleic Acids Research19:6565-6572), Hidden Markov Models (HMM; Eddy, S. R. (1996) Cur. Opin.Str. Biol. 6:361-365; Sonnhammer et al. (1997) Proteins 28:405-420), andthe like, can be used to manipulate and analyze polynucleotide andpolypeptide sequences encoded by polynucleotides. These databases,algorithms and other methods are well known in the art and are describedin Ausubel et al. (1997; Short Protocols in Molecular Biology, JohnWiley & Sons, New York N.Y., unit 7.7) and in Meyers, R. A. (1995;Molecular Biology and Biotechnology, Wiley VCH, New York N.Y., p856-853).

Furthermore, methods using manual alignment of sequences similar orhomologous to one or more polynucleotide sequences or one or morepolypeptides encoded by the polynucleotide sequences may be used toidentify regions of similarity and conserved domains. Such manualmethods are well-known of those of skill in the art and can include, forexample, comparisons of tertiary structure between a polypeptidesequence encoded by a polynucleotide which comprises a known functionwith a polypeptide sequence encoded by a polynucleotide sequence whichhas a function not yet determined. Such examples of tertiary structuremay comprise predicted alpha helices, beta-sheets, amphipathic helices,leucine zipper motifs, zinc finger motifs, proline-rich regions,cysteine repeat motifs, and the like.

VI. IDENTIFYING POLYNUCLEOTIDES OR NUCLEIC ACIDS BY HYBRIDIZATION

Polynucleotides homologous to the sequences illustrated in the SequenceListing and tables can be identified, e.g., by hybridization to eachother under stringent or under highly stringent conditions. Singlestranded polynucleotides hybridize when they associate based on avariety of well characterized physical-chemical forces, such as hydrogenbonding, solvent exclusion, base stacking and the like. The stringencyof a hybridization reflects the degree of sequence identity of thenucleic acids involved, such that the higher the stringency, the moresimilar are the two polynucleotide strands. Stringency is influenced bya variety of factors, including temperature, salt concentration andcomposition, organic and non-organic additives, solvents, etc. presentin both the hybridization and wash solutions and incubations (and numberthereof), as described in more detail in the references cited above.Encompassed by the invention are polynucleotide sequences that arecapable of hybridizing to the claimed polynucleotide sequences, and, inparticular, to those shown in SEQ ID NOs: 860; 802; 240; 274; 558; 24;1120; 44; 460; 286; 120; 130; 134; 698; 832; 580; 612; 48, and fragmentsthereof under various conditions of stringency. (See, e.g., Wahl, G. M.and S. L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A. R.(1987) Methods Enzymol. 152:507-511.) Estimates of homology are providedby either DNA-DNA or DNA-RNA hybridization under conditions ofstringency as is well understood by those skilled in the art (Hames andHiggins, Eds. (1985) Nucleic Acid Hybridisation, IRL Press, Oxford,U.K.). Stringency conditions can be adjusted to screen for moderatelysimilar fragments, such as homologous sequences from distantly relatedorganisms, to highly similar fragments, such as genes that duplicatefunctional enzymes from closely related organisms. Post-hybridizationwashes determine stringency conditions.

In addition to the nucleotide sequences listed in Tables 4 and 5, fulllength cDNA, orthologs, paralogs and homologs of the present nucleotidesequences may be identified and isolated using well known methods. ThecDNA libraries orthologs, paralogs and homologs of the presentnucleotide sequences may be screened using hybridization methods todetermine their utility as hybridization target or amplification probes.

An example of stringent hybridization conditions for hybridization ofcomplementary nucleic acids which have more than 100 complementaryresidues on a filter in a Southern or northern blot is about 5° C. to20° C. lower than the thermal melting point (T_(m)) for the specificsequence at a defined ionic strength and pH. The T_(m) is thetemperature (under defined ionic strength and pH) at which 50% of thetarget sequence hybridizes to a perfectly matched probe. Nucleic acidmolecules that hybridize under stringent conditions will typicallyhybridize to a probe based on either the entire cDNA or selectedportions, e.g., to a unique subsequence, of the cDNA under washconditions of 0.2×SSC to 2.0×SSC, 0.1% SDS at 50-65° C. For example,high stringency is about 0.2×SSC, 0.1% SDS at 65° C. Ultra-highstringency will be the same conditions except the wash temperature israised about 3 to about 5° C., and ultra-ultra-high stringency will bethe same conditions except the wash temperature is raised about 6 toabout 9° C. For identification of less closely related homologues washescan be performed at a lower temperature, e.g., 50° C. In general,stringency is increased by raising the wash temperature and/ordecreasing the concentration of SSC, as known in the art.

In another example, stringent salt concentration will ordinarily be lessthan about 750 mM NaCl and 75 mM trisodium citrate, preferably less thanabout 500 mM NaCl and 50 mM trisodium citrate, and most preferably lessthan about 250 mM NaCl and 25 mM trisodium citrate. Low stringencyhybridization can be obtained in the absence of organic solvent, e.g.,formamide, while high stringency hybridization can be obtained in thepresence of at least about 35% formamide, and most preferably at leastabout 50% formamide. Stringent temperature conditions will ordinarilyinclude temperatures of at least about 30° C., more preferably of atleast about 37° C., and most preferably of at least about 42° C. Varyingadditional parameters, such as hybridization time, the concentration ofdetergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion orexclusion of carrier DNA, are well known to those skilled in the art.Various levels of stringency are accomplished by combining these variousconditions as needed. In a preferred embodiment, hybridization willoccur at 30° C. in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. Ina more preferred embodiment, hybridization will occur at 37° C. in 500mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and 100 μg/mldenatured salmon sperm DNA (ssDNA). In a most preferred embodiment,hybridization will occur at 42° C. in 250 mM NaCl, 25 mM trisodiumcitrate, 1% SDS, 50% formamide, and 200 μg/ml ssDNA. Useful variationson these conditions will be readily apparent to those skilled in theart.

The washing steps that follow hybridization can also vary in stringency.Wash stringency conditions can be defined by salt concentration and bytemperature. As above, wash stringency can be increased by decreasingsalt concentration or by increasing temperature. For example, stringentsalt concentration for the wash steps will preferably be less than about30 mM NaCl and 3 mM trisodium citrate, and most preferably less thanabout 15 mM NaCl and 1.5 mM trisodium citrate. Stringent temperatureconditions for the wash steps will ordinarily include temperature of atleast about 25° C., more preferably of at least about 42° C. Anotherpreferred set of highly stringent conditions uses two final washes in0.1×SSC, 0.1% SDS at 65° C. The most preferred high stringency washesare of at least about 68° C. For example, in a preferred embodiment,wash steps will occur at 25° C. in 30 mM NaCl, 3 mM trisodium citrate,and 0.1% SDS. In a more preferred embodiment, wash steps will occur at42° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In a mostpreferred embodiment, the wash steps will occur at 68° C. in 15 mM NaCl,1.5 mM trisodium citrate, and 0.1% SDS. Additional variations on theseconditions will be readily apparent to those skilled in the art (seeU.S. Patent Application No. 20010010913).

As another example, stringent conditions can be selected such that anoligonucleotide that is perfectly complementary to the codingoligonucleotide hybridizes to the coding oligonucleotide with at leastabout a 5-10× higher signal to noise ratio than the ratio forhybridization of the perfectly complementary oligonucleotide to anucleic acid encoding a transcription factor known as of the filing dateof the application. Conditions can be selected such that a higher signalto noise ratio is observed in the particular assay which is used, e.g.,about 15×, 25×, 35×, 50× or more. Accordingly, the subject nucleic acidhybridizes to the unique coding oligonucleotide with at least a 2×higher signal to noise ratio as compared to hybridization of the codingoligonucleotide to a nucleic acid encoding known polypeptide. Again,higher signal to noise ratios can be selected, e.g., about 5×, 10×, 25×,35×, 50× or more. The particular signal will depend on the label used inthe relevant assay, e.g., a fluorescent label, a colorimetric label, aradioactive label, or the like.

Alternatively, transcription factor homolog polypeptides can be obtainedby screening an expression library using antibodies specific for one ormore transcription factors. With the provision herein of the disclosedtranscription factor, and transcription factor homologue nucleic acidsequences, the encoded polypeptide(s) can be expressed and purified in aheterologous expression system (e.g., E. coli) and used to raiseantibodies (monoclonal or polyclonal) specific for the polypeptide(s) inquestion. Antibodies can also be raised against synthetic peptidesderived from transcription factor, or transcription factor homologue,amino acid sequences. Methods of raising antibodies are well known inthe art and are described in Harlow and Lane (1988) Antibodies: ALaboratory Manual, Cold Spring Harbor Laboratory, New York. Suchantibodies can then be used to screen an expression library producedfrom the plant from which it is desired to clone additionaltranscription factor homologues, using the methods described above. Theselected cDNAs can be confirmed by sequencing and enzymatic activity.

VII. SEQUENCE VARIATIONS

It will readily be appreciated by those of skill in the art, that any ofa variety of polynucleotide sequences are capable of encoding thetranscription factors and transcription factor homologue polypeptides ofthe invention. Due to the degeneracy of the genetic code, many differentpolynucleotides can encode identical and/or substantially similarpolypeptides in addition to those sequences illustrated in the SequenceListing. Nucleic acids having a sequence that differs from the sequencesshown in the Sequence Listing, or complementary sequences, that encodefunctionally equivalent peptides (i.e., peptides having some degree ofequivalent or similar biological activity) but differ in sequence fromthe sequence shown in the sequence listing due to degeneracy in thegenetic code, are also within the scope of the invention.

Altered polynucleotide sequences encoding polypeptides include thosesequences with deletions, insertions, or substitutions of differentnucleotides, resulting in a polynucleotide encoding a polypeptide withat least one functional characteristic of the instant polypeptides.Included within this definition are polymorphisms which may or may notbe readily detectable using a particular oligonucleotide probe of thepolynucleotide encoding the instant polypeptides, and improper orunexpected hybridization to allelic variants, with a locus other thanthe normal chromosomal locus for the polynucleotide sequence encodingthe instant polypeptides.

Allelic variant refers to any of two or more alternative forms of a geneoccupying the same chromosomal locus. Allelic variation arises naturallythrough mutation, and may result in phenotypic polymorphism withinpopulations. Gene mutations can be silent (i.e., no change in theencoded polypeptide) or may encode polypeptides having altered aminoacid sequence. The term allelic variant is also used herein to denote aprotein encoded by an allelic variant of a gene. Splice variant refersto alternative forms of RNA transcribed from a gene. Splice variationarises naturally through use of alternative splicing sites within atranscribed RNA molecule, or less commonly between separatelytranscribed RNA molecules, and may result in several mRNAs transcribedfrom the same gene. Splice variants may encode polypeptides havingaltered amino acid sequence. The term splice variant is also used hereinto denote a protein encoded by a splice variant of an mRNA transcribedfrom a gene.

Those skilled in the art would recognize that G681, SEQ ID NO: 580,represents a single transcription factor; allelic variation andalternative splicing may be expected to occur. Allelic variants of SEQID NO: 579 can be cloned by probing cDNA or genomic libraries fromdifferent individual organisms according to standard procedures. Allelicvariants of the DNA sequence shown in SEQ ID NO: 579, including thosecontaining silent mutations and those in which mutations result in aminoacid sequence changes, are within the scope of the present invention, asare proteins which are allelic variants of SEQ ID NO: 580. cDNAsgenerated from alternatively spliced mRNAs, which retain the propertiesof the transcription factor are included within the scope of the presentinvention, as are polypeptides encoded by such cDNAs and mRNAs. Allelicvariants and splice variants of these sequences can be cloned by probingcDNA or genomic libraries from different individual organisms or tissuesaccording to standard procedures known in the art (see U.S. Pat. No.6,388,064).

For example, Table 1 illustrates, e.g., that the codons AGC, AGT, TCA,TCC, TCG, and TCT all encode the same amino acid: serine. Accordingly,at each position in the sequence where there is a codon encoding serine,any of the above trinucleotide sequences can be used without alteringthe encoded polypeptide.

TABLE 1 Amino acid Possible Codons Alanine Ala A GCA GCC GCG GCUCysteine Cys C TGC TGT Aspartic acid Asp D GAC GAT Glutamic acid Glu EGAA GAG Phenylalanine Phe F TTC TTT Glycine Gly G GGA GGC GGG GGTHistidine His H CAC CAT Isoleucine Ile I ATA ATC ATT Lysine Lys K AAAAAG Leucine Leu L TTA TTG CTA CTC CTG CTT Methionine Met M ATGAsparagine Asn N AAC AAT Proline Pro P CCA CCC CCG CCT Glutamine Gln QCAA CAG Arginine Arg R AGA AGG CGA CGC CGG CGT Serine Ser S AGC AGT TCATCC TCG TCT Threonine Thr T ACA ACC ACG ACT Valine Val V GTA GTC GTG GTTTryptophan Trp W TGG Tyrosine Tyr Y TAC TAT

Sequence alterations that do not change the amino acid sequence encodedby the polynucleotide are termed “silent” variations. With the exceptionof the codons ATG and TGG, encoding methionine and tryptophan,respectively, any of the possible codons for the same amino acid can besubstituted by a variety of techniques, e.g., site-directed mutagenesis,available in the art. Accordingly, any and all such variations of asequence selected from the above table are a feature of the invention.

In addition to silent variations, other conservative variations thatalter one, or a few amino acids in the encoded polypeptide, can be madewithout altering the function of the polypeptide, these conservativevariants are, likewise, a feature of the invention.

For example, substitutions, deletions and insertions introduced into thesequences provided in the Sequence Listing are also envisioned by theinvention. Such sequence modifications can be engineered into a sequenceby site-directed mutagenesis (Wu (ed.) Meth. Enzymol. (1993) vol. 217,Academic Press) or the other methods noted below. Amino acidsubstitutions are typically of single residues; insertions usually willbe on the order of about from 1 to 10 amino acid residues; and deletionswill range about from 1 to 30 residues. In preferred embodiments,deletions or insertions are made in adjacent pairs, e.g., a deletion oftwo residues or insertion of two residues. Substitutions, deletions,insertions or any combination thereof can be combined to arrive at asequence. The mutations that are made in the polynucleotide encoding thetranscription factor should not place the sequence out of reading frameand should not create complementary regions that could produce secondarymRNA structure. Preferably, the polypeptide encoded by the DNA performsthe desired function.

Conservative substitutions are those in which at least one residue inthe amino acid sequence has been removed and a different residueinserted in its place. Such substitutions generally are made inaccordance with the Table 2 when it is desired to maintain the activityof the protein. Table 2 shows amino acids which can be substituted foran amino acid in a protein and which are typically regarded asconservative substitutions.

TABLE 2 Conservative Residue Substitutions Ala Ser Arg Lys Asn Gln; HisAsp Glu Gln Asn Cys Ser Glu Asp Gly Pro His Asn; Gln Ile Leu, Val LeuIle; Val Lys Arg; Gln Met Leu; Ile Phe Met; Leu; Tyr Ser Thr; Gly ThrSer; Val Trp Tyr Tyr Trp; Phe Val Ile; Leu

Similar substitutions are those in which at least one residue in theamino acid sequence has been removed and a different residue inserted inits place. Such substitutions generally are made in accordance with theTable 3 when it is desired to maintain the activity of the protein.Table 3 shows amino acids which can be substituted for an amino acid ina protein and which are typically regarded as structural and functionalsubstitutions. For example, a residue in column 1 of Table 3 may besubstituted with residue in column 2; in addition, a residue in column 2of Table 3 may be substituted with the residue of column 1.

TABLE 3 Residue Similar Substitutions Ala Ser; Thr; Gly; Val; Leu; IleArg Lys; His; Gly Asn Gln; His; Gly; Ser; Thr Asp Glu, Ser; Thr Gln Asn;Ala Cys Ser; Gly Glu Asp Gly Pro; Arg His Asn; Gln; Tyr; Phe; Lys; ArgIle Ala; Leu; Val; Gly; Met Leu Ala; Ile; Val; Gly; Met Lys Arg; His;Gln; Gly; Pro Met Leu; Ile; Phe Phe Met; Leu; Tyr; Trp; His; Val; AlaSer Thr; Gly; Asp; Ala; Val; Ile; His Thr Ser; Val; Ala; Gly Trp Tyr;Phe; His Tyr Trp; Phe; His Val Ala; Ile; Leu; Gly; Thr; Ser; Glu

Substitutions that are less conservative than those in Table 2 can beselected by picking residues that differ more significantly in theireffect on maintaining (a) the structure of the polypeptide backbone inthe area of the substitution, for example, as a sheet or helicalconformation, (b) the charge or hydrophobicity of the molecule at thetarget site, or (c) the bulk of the side chain. The substitutions whichin general are expected to produce the greatest changes in proteinproperties will be those in which (a) a hydrophilic residue, e.g., serylor threonyl, is substituted for (or by) a hydrophobic residue, e.g.,leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine orproline is substituted for (or by) any other residue; (c) a residuehaving an electropositive side chain, e.g., lysyl, arginyl, or histidyl,is substituted for (or by) an electronegative residue, e.g., glutamyl oraspartyl; or (d) a residue having a bulky side chain, e.g.,phenylalanine, is substituted for (or by) one not having a side chain,e.g., glycine.

VIII. FURTHER MODIFYING SEQUENCES OF THE INVENTION Mutation/ForcedEvolution

In addition to generating silent or conservative substitutions as noted,above, the present invention optionally includes methods of modifyingthe sequences of the Sequence Listing. In the methods, nucleic acid orprotein modification methods are used to alter the given sequences toproduce new sequences and/or to chemically or enzymatically modify givensequences to change the properties of the nucleic acids or proteins.

Thus, in one embodiment, given nucleic acid sequences are modified,e.g., according to standard mutagenesis or artificial evolution methodsto produce modified sequences. The modified sequences may be createdusing purified natural polynucleotides isolated from any organism or maybe synthesized from purified compositions and chemicals using chemicalmeans well know to those of skill in the art. For example, Ausubel,supra, provides additional details on mutagenesis methods. Artificialforced evolution methods are described, for example, by Stemmer (1994)Nature 370:389-391, Stemmer (1994) Proc. Natl. Acad. Sci. USA91:10747-10751, and U.S. Pat. Nos. 5,811,238, 5,837,500, and 6,242,568.Methods for engineering synthetic transcription factors and otherpolypeptides are described, for example, by Zhang et al. (2000) J. Biol.Chem. 275:33850-33860, Liu et al. (2001) J. Biol. Chem. 276:11323-11334,and Isalan et al. (2001) Nature Biotechnol. 19:656-660. Many othermutation and evolution methods are also available and expected to bewithin the skill of the practitioner.

Similarly, chemical or enzymatic alteration of expressed nucleic acidsand polypeptides can be performed by standard methods. For example,sequence can be modified by addition of lipids, sugars, peptides,organic or inorganic compounds, by the inclusion of modified nucleotidesor amino acids, or the like. For example, protein modificationtechniques are illustrated in Ausubel, supra. Further details onchemical and enzymatic modifications can be found herein. Thesemodification methods can be used to modify any given sequence, or tomodify any sequence produced by the various mutation and artificialevolution modification methods noted herein.

Accordingly, the invention provides for modification of any givennucleic acid by mutation, evolution, chemical or enzymatic modification,or other available methods, as well as for the products produced bypracticing such methods, e.g., using the sequences herein as a startingsubstrate for the various modification approaches.

For example, optimized coding sequence containing codons preferred by aparticular prokaryotic or eukaryotic host can be used e.g., to increasethe rate of translation or to produce recombinant RNA transcripts havingdesirable properties, such as a longer half-life, as compared withtranscripts produced using a non-optimized sequence. Translation stopcodons can also be modified to reflect host preference. For example,preferred stop codons for Saccharomyces cerevisiae and mammals are TAAand TGA, respectively. The preferred stop codon for monocotyledonousplants is TGA, whereas insects and E. coli prefer to use TAA as the stopcodon.

The polynucleotide sequences of the present invention can also beengineered in order to alter a coding sequence for a variety of reasons,including but not limited to, alterations which modify the sequence tofacilitate cloning, processing and/or expression of the gene product.For example, alterations are optionally introduced using techniqueswhich are well known in the art, e.g., site-directed mutagenesis, toinsert new restriction sites, to alter glycosylation patterns, to changecodon preference, to introduce splice sites, etc.

Furthermore, a fragment or domain derived from any of the polypeptidesof the invention can be combined with domains derived from othertranscription factors or synthetic domains to modify the biologicalactivity of a transcription factor. For instance, a DNA-binding domainderived from a transcription factor of the invention can be combinedwith the activation domain of another transcription factor or with asynthetic activation domain. A transcription activation domain assistsin initiating transcription from a DNA-binding site. Examples includethe transcription activation region of VP16 or GAL4 (Moore et al. (1998)Proc. Natl. Acad. Sci. USA 95: 376-381; and Aoyama et al. (1995) PlantCell 7:1773-1785), peptides derived from bacterial sequences (Ma andPtashne (1987) Cell 51; 113-119) and synthetic peptides (Giniger andPtashne, (1987) Nature 330:670-672).

IX. EXPRESSION AND MODIFICATION OF POLYPEPTIDES

Typically, polynucleotide sequences of the invention are incorporatedinto recombinant DNA (or RNA) molecules that direct expression ofpolypeptides of the invention in appropriate host cells, transgenicplants, in vitro translation systems, or the like. Due to the inherentdegeneracy of the genetic code, nucleic acid sequences which encodesubstantially the same or a functionally equivalent amino acid sequencecan be substituted for any listed sequence to provide for cloning andexpressing the relevant homologue.

X. VECTORS, PROMOTERS, AND EXPRESSION SYSTEMS

The present invention includes recombinant constructs comprising one ormore of the nucleic acid sequences herein. The constructs typicallycomprise a vector, such as a plasmid, a cosmid, a phage, a virus (e.g.,a plant virus), a bacterial artificial chromosome (BAC), a yeastartificial chromosome (YAC), or the like, into which a nucleic acidsequence of the invention has been inserted, in a forward or reverseorientation. In a preferred aspect of this embodiment, the constructfurther comprises regulatory sequences, including, for example, apromoter, operably linked to the sequence. Large numbers of suitablevectors and promoters are known to those of skill in the art, and arecommercially available.

General texts that describe molecular biological techniques usefulherein, including the use and production of vectors, promoters and manyother relevant topics, include Berger, Sambrook and Ausubel, supra. Anyof the identified sequences can be incorporated into a cassette orvector, e.g., for expression in plants. A number of expression vectorssuitable for stable transformation of plant cells or for theestablishment of transgenic plants have been described including thosedescribed in Weissbach and Weissbach, (1989) Methods for Plant MolecularBiology, Academic Press, and Gelvin et al., (1990) Plant MolecularBiology Manual, Kluwer Academic Publishers. Specific examples includethose derived from a Ti plasmid of Agrobacterium tumefaciens, as well asthose disclosed by Herrera-Estrella et al. (1983) Nature 303: 209, Bevan(1984) Nucl Acid Res. 12: 8711-8721, Klee (1985) Bio/Technology 3:637-642, for dicotyledonous plants.

Alternatively, non-Ti vectors can be used to transfer the DNA intomonocotyledonous plants and cells by using free DNA delivery techniques.Such methods can involve, for example, the use of liposomes,electroporation, microprojectile bombardment, silicon carbide whiskers,and viruses. By using these methods transgenic plants such as wheat,rice (Christou (1991) Bio/Technology 9: 957-962) and corn (Gordon-Kamm(1990) Plant Cell 2: 603-618) can be produced. An immature embryo canalso be a good target tissue for monocots for direct DNA deliverytechniques by using the particle gun (Weeks et al. (1993) Plant Physiol102: 1077-1084; Vasil (1993) Bio/Technology 10: 667-674; Wan and Lemeaux(1994) Plant Physiol 104: 37-48, and for Agrobacterium-mediated DNAtransfer (Ishida et al. (1996) Nature Biotech 14: 745-750).

Typically, plant transformation vectors include one or more cloned plantcoding sequence (genomic or cDNA) under the transcriptional control of5′ and 3′ regulatory sequences and a dominant selectable marker. Suchplant transformation vectors typically also contain a promoter (e.g., aregulatory region controlling inducible or constitutive,environmentally- or developmentally-regulated, or cell- ortissue-specific expression), a transcription initiation start site, anRNA processing signal (such as intron splice sites), a transcriptiontermination site, and/or a polyadenylation signal.

Examples of constitutive plant promoters which can be useful forexpressing the TF sequence include: the cauliflower mosaic virus (CaMV)35S promoter, which confers constitutive, high-level expression in mostplant tissues (see, e.g., Odell et al. (1985) Nature 313:810-812); thenopaline synthase promoter (An et al. (1988) Plant Physiol 88:547-552);and the octopine synthase promoter (Fromm et al. (1989) Plant Cell 1:977-984).

A variety of plant gene promoters that regulate gene expression inresponse to environmental, hormonal, chemical, developmental signals,and in a tissue-active manner can be used for expression of a TFsequence in plants. Choice of a promoter is based largely on thephenotype of interest and is determined by such factors as tissue (e.g.,seed, fruit, root, pollen, vascular tissue, flower, carpel, etc.),inducibility (e.g., in response to wounding, heat, cold, drought, light,pathogens, etc.), timing, developmental stage, and the like. Numerousknown promoters have been characterized and can favorably be employed topromote expression of a polynucleotide of the invention in a transgenicplant or cell of interest. For example, tissue specific promotersinclude: seed-specific promoters (such as the napin, phaseolin or DC3promoter described in U.S. Pat. No. 5,773,697), fruit-specific promotersthat are active during fruit ripening (such as the dru 1 promoter (U.S.Pat. No. 5,783,393), or the 2A11 promoter (U.S. Pat. No. 4,943,674) andthe tomato polygalacturonase promoter (Bird et al. (1988) Plant Mol Biol11:651), root-specific promoters, such as those disclosed in U.S. Pat.Nos. 5,618,988, 5,837,848 and 5,905,186, pollen-active promoters such asPTA29, PTA26 and PTA13 (U.S. Pat. No. 5,792,929), promoters active invascular tissue (Ringli and Keller (1998) Plant Mol Biol 37:977-988),flower-specific (Kaiser et al, (1995) Plant Mol Biol 28:231-243), pollen(Baerson et al. (1994) Plant Mol Biol 26:1947-1959), carpels (Ohl et al.(1990) Plant Cell 2:837-848), pollen and ovules (Baerson et al. (1993)Plant Mol Biol 22:255-267), auxin-inducible promoters (such as thatdescribed in van der Kop et al. (1999) Plant Mol Biol 39:979-990 orBaumann et al. (1999) Plant Cell 11:323-334), cytokinin-induciblepromoter (Guevara-Garcia (1998) Plant Mol Biol 38:743-753), promotersresponsive to gibberellin (Shi et al. (1998) Plant Mol Biol38:1053-1060, Willmott et al. (1998) 38:817-825) and the like.Additional promoters are those that elicit expression in response toheat (Ainley et al. (1993) Plant Mol Biol 22: 13-23), light (e.g., thepea rbcS-3A promoter, Kuhlemeier et al. (1989) Plant Cell 1:471, and themaize rbcS promoter, Schaffner and Sheen (1991) Plant Cell 3: 997);wounding (e.g., wunI, Siebertz et al. (1989) Plant Cell 1: 961);pathogens (such as the PR-1 promoter described in Buchel et al. (1999)Plant Mol. Biol. 40:387-396, and the PDF1.2 promoter described inManners et al. (1998) Plant Mol. Biol. 38:1071-80), and chemicals suchas methyl jasmonate or salicylic acid (Gatz et al. (1997) Plant Mol Biol48: 89-108). In addition, the timing of the expression can be controlledby using promoters such as those acting at senescence (An and Amazon(1995) Science 270: 1986-1988); or late seed development (Odell et al.(1994) Plant Physiol 106:447-458).

Plant expression vectors can also include RNA processing signals thatcan be positioned within, upstream or downstream of the coding sequence.In addition, the expression vectors can include additional regulatorysequences from the 3′-untranslated region of plant genes, e.g., a 3′terminator region to increase mRNA stability of the mRNA, such as thePI-II terminator region of potato or the octopine or nopaline synthase3′ terminator regions.

Additional Expression Elements

Specific initiation signals can aid in efficient translation of codingsequences. These signals can include, e.g., the ATG initiation codon andadjacent sequences. In cases where a coding sequence, its initiationcodon and upstream sequences are inserted into the appropriateexpression vector, no additional translational control signals may beneeded. However, in cases where only coding sequence (e.g., a matureprotein coding sequence), or a portion thereof, is inserted, exogenoustranscriptional control signals including the ATG initiation codon canbe separately provided. The initiation codon is provided in the correctreading frame to facilitate transcription. Exogenous transcriptionalelements and initiation codons can be of various origins, both naturaland synthetic. The efficiency of expression can be enhanced by theinclusion of enhancers appropriate to the cell system in use.

Expression Hosts

The present invention also relates to host cells which are transducedwith vectors of the invention, and the production of polypeptides of theinvention (including fragments thereof) by recombinant techniques. Hostcells are genetically engineered (i.e., nucleic acids are introduced,e.g., transduced, transformed or transfected) with the vectors of thisinvention, which may be, for example, a cloning vector or an expressionvector comprising the relevant nucleic acids herein. The vector isoptionally a plasmid, a viral particle, a phage, a naked nucleic acid,etc. The engineered host cells can be cultured in conventional nutrientmedia modified as appropriate for activating promoters, selectingtransformants, or amplifying the relevant gene. The culture conditions,such as temperature, pH and the like, are those previously used with thehost cell selected for expression, and will be apparent to those skilledin the art and in the references cited herein, including, Sambrook andAusubel.

The host cell can be a eukaryotic cell, such as a yeast cell, or a plantcell, or the host cell can be a prokaryotic cell, such as a bacterialcell. Plant protoplasts are also suitable for some applications. Forexample, the DNA fragments are introduced into plant tissues, culturedplant cells or plant protoplasts by standard methods includingelectroporation (Fromm et al., (1985) Proc. Natl. Acad. Sci. USA 82,5824, infection by viral vectors such as cauliflower mosaic virus (CaMV)(Hohn et al., (1982) Molecular Biology of Plant Tumors, (Academic Press,New York) pp. 549-560; U.S. Pat. No. 4,407,956), high velocity ballisticpenetration by small particles with the nucleic acid either within thematrix of small beads or particles, or on the surface (Klein et al.,(1987) Nature 327, 70-73), use of pollen as vector (WO 85/01856), or useof Agrobacterium tumefaciens or A. rhizogenes carrying a T-DNA plasmidin which DNA fragments are cloned. The T-DNA plasmid is transmitted toplant cells upon infection by Agrobacterium tumefaciens, and a portionis stably integrated into the plant genome (Horsch et al. (1984) Science233:496-498; Fraley et al. (1983) Proc. Natl. Acad. Sci. USA 80, 4803).

The cell can include a nucleic acid of the invention which encodes apolypeptide, wherein the cells expresses a polypeptide of the invention.The cell can also include vector sequences, or the like. Furthermore,cells and transgenic plants that include any polypeptide or nucleic acidabove or throughout this specification, e.g., produced by transductionof a vector of the invention, are an additional feature of theinvention.

For long-term, high-yield production of recombinant proteins, stableexpression can be used. Host cells transformed with a nucleotidesequence encoding a polypeptide of the invention are optionally culturedunder conditions suitable for the expression and recovery of the encodedprotein from cell culture. The protein or fragment thereof produced by arecombinant cell may be secreted, membrane-bound, or containedintracellularly, depending on the sequence and/or the vector used. Aswill be understood by those of skill in the art, expression vectorscontaining polynucleotides encoding mature proteins of the invention canbe designed with signal sequences which direct secretion of the maturepolypeptides through a prokaryotic or eukaryotic cell membrane.

XI. MODIFIED AMINO ACID RESIDUES

Polypeptides of the invention may contain one or more modified aminoacid residues. The presence of modified amino acids may be advantageousin, for example, increasing polypeptide half-life, reducing polypeptideantigenicity or toxicity, increasing polypeptide storage stability, orthe like. Amino acid residue(s) are modified, for example,co-translationally or post-translationally during recombinant productionor modified by synthetic or chemical means.

Non-limiting examples of a modified amino acid residue includeincorporation or other use of acetylated amino acids, glycosylated aminoacids, sulfated amino acids, prenylated (e.g., farnesylated,geranylgeranylated) amino acids, PEG modified (e.g., “PEGylated”) aminoacids, biotinylated amino acids, carboxylated amino acids,phosphorylated amino acids, etc. References adequate to guide one ofskill in the modification of amino acid residues are replete throughoutthe literature.

The modified amino acid residues may prevent or increase affinity of thepolypeptide for another molecule, including, but not limited to,polynucleotide, proteins, carbohydrates, lipids and lipid derivatives,and other organic or synthetic compounds.

XII. IDENTIFICATION OF ADDITIONAL FACTORS

A transcription factor provided by the present invention can also beused to identify additional endogenous or exogenous molecules that canaffect a phentoype or trait of interest. On the one hand, such moleculesinclude organic (small or large molecules) and/or inorganic compoundsthat affect expression of (i.e., regulate) a particular transcriptionfactor. Alternatively, such molecules include endogenous molecules thatare acted upon either at a transcriptional level by a transcriptionfactor of the invention to modify a phenotype as desired. For example,the transcription factors can be employed to identify one or moredownstream gene with which is subject to a regulatory effect of thetranscription factor. In one approach, a transcription factor ortranscription factor homologue of the invention is expressed in a hostcell, e.g., a transgenic plant cell, tissue or explant, and expressionproducts, either RNA or protein, of likely or random targets aremonitored, e.g., by hybridization to a microarray of nucleic acid probescorresponding to genes expressed in a tissue or cell type of interest,by two-dimensional gel electrophoresis of protein products, or by anyother method known in the art for assessing expression of gene productsat the level of RNA or protein. Alternatively, a transcription factor ofthe invention can be used to identify promoter sequences (i.e., bindingsites) involved in the regulation of a downstream target. Afteridentifying a promoter sequence, interactions between the transcriptionfactor and the promoter sequence can be modified by changing specificnucleotides in the promoter sequence or specific amino acids in thetranscription factor that interact with the promoter sequence to alter aplant trait. Typically, transcription factor DNA-binding sites areidentified by gel shift assays. After identifying the promoter regions,the promoter region sequences can be employed in double-stranded DNAarrays to identify molecules that affect the interactions of thetranscription factors with their promoters (Bulyk et al. (1999) NatureBiotechnology 17:573-577).

The identified transcription factors are also useful to identifyproteins that modify the activity of the transcription factor. Suchmodification can occur by covalent modification, such as byphosphorylation, or by protein-protein (homo or -heteropolymer)interactions. Any method suitable for detecting protein-proteininteractions can be employed. Among the methods that can be employed areco-immunoprecipitation, cross-linking and co-purification throughgradients or chromatographic columns, and the two-hybrid yeast system.

The two-hybrid system detects protein interactions in vivo and isdescribed in Chien et al. ((1991), Proc. Natl. Acad. Sci. USA88:9578-9582) and is commercially available from Clontech (Palo Alto,Calif.). In such a system, plasmids are constructed that encode twohybrid proteins: one consists of the DNA-binding domain of atranscription activator protein fused to the TF polypeptide and theother consists of the transcription activator protein's activationdomain fused to an unknown protein that is encoded by a cDNA that hasbeen recombined into the plasmid as part of a cDNA library. TheDNA-binding domain fusion plasmid and the cDNA library are transformedinto a strain of the yeast Saccharomyces cerevisiae that contains areporter gene (e.g., lacZ) whose regulatory region contains thetranscription activator's binding site. Either hybrid protein alonecannot activate transcription of the reporter gene. Interaction of thetwo hybrid proteins reconstitutes the functional activator protein andresults in expression of the reporter gene, which is detected by anassay for the reporter gene product. Then, the library plasmidsresponsible for reporter gene expression are isolated and sequenced toidentify the proteins encoded by the library plasmids. After identifyingproteins that interact with the transcription factors, assays forcompounds that interfere with the TF protein-protein interactions can bepreformed.

XIII. IDENTIFICATION OF MODULATORS

In addition to the intracellular molecules described above,extracellular molecules that alter activity or expression of atranscription factor, either directly or indirectly, can be identified.For example, the methods can entail first placing a candidate moleculein contact with a plant or plant cell. The molecule can be introduced bytopical administration, such as spraying or soaking of a plant, and thenthe molecule's effect on the expression or activity of the TFpolypeptide or the expression of the polynucleotide monitored. Changesin the expression of the TF polypeptide can be monitored by use ofpolyclonal or monoclonal antibodies, gel electrophoresis or the like.Changes in the expression of the corresponding polynucleotide sequencecan be detected by use of microarrays, Northerns, quantitative PCR, orany other technique for monitoring changes in mRNA expression. Thesetechniques are exemplified in Ausubel et al. (eds) Current Protocols inMolecular Biology, John Wiley & Sons (1998, and supplements through2001). Such changes in the expression levels can be correlated withmodified plant traits and thus identified molecules can be useful forsoaking or spraying on fruit, vegetable and grain crops to modify traitsin plants.

Essentially any available composition can be tested for modulatoryactivity of expression or activity of any nucleic acid or polypeptideherein. Thus, available libraries of compounds such as chemicals,polypeptides, nucleic acids and the like can be tested for modulatoryactivity. Often, potential modulator compounds can be dissolved inaqueous or organic (e.g., DMSO-based) solutions for easy delivery to thecell or plant of interest in which the activity of the modulator is tobe tested. Optionally, the assays are designed to screen large modulatorcomposition libraries by automating the assay steps and providingcompounds from any convenient source to assays, which are typically runin parallel (e.g., in microtiter formats on microtiter plates in roboticassays).

In one embodiment, high throughput screening methods involve providing acombinatorial library containing a large number of potential compounds(potential modulator compounds). Such “combinatorial chemical libraries”are then screened in one or more assays, as described herein, toidentify those library members (particular chemical species orsubclasses) that display a desired characteristic activity. Thecompounds thus identified can serve as target compounds.

A combinatorial chemical library can be, e.g., a collection of diversechemical compounds generated by chemical synthesis or biologicalsynthesis. For example, a combinatorial chemical library such as apolypeptide library is formed by combining a set of chemical buildingblocks (e.g., in one example, amino acids) in every possible way for agiven compound length (i.e., the number of amino acids in a polypeptidecompound of a set length). Exemplary libraries include peptidelibraries, nucleic acid libraries, antibody libraries (see, e.g., Vaughnet al. (1996) Nature Biotechnology, 14(3):309-314 and PCT/US96/10287),carbohydrate libraries (see, e.g., Liang et al. Science (1996)274:1520-1522 and U.S. Pat. No. 5,593,853), peptide nucleic acidlibraries (see, e.g., U.S. Pat. No. 5,539,083), and small organicmolecule libraries (see, e.g., benzodiazepines, Baum C&EN January 18,page 33 (1993); isoprenoids, U.S. Pat. No. 5,569,588; thiazolidinonesand metathiazanones, U.S. Pat. No. 5,549,974; pyrrolidines, U.S. Pat.Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Pat. No.5,506,337) and the like.

Preparation and screening of combinatorial or other libraries is wellknown to those of skill in the art. Such combinatorial chemicallibraries include, but are not limited to, peptide libraries (see, e.g.,U.S. Pat. No. 5,010,175; Furka, (1991) Int. J. Pept. Prot. Res.37:487-493; and Houghton et al. (1991) Nature 354:84-88). Otherchemistries for generating chemical diversity libraries can also beused.

In addition, as noted, compound screening equipment for high-throughputscreening is generally available, e.g., using any of a number of wellknown robotic systems that have also been developed for solution phasechemistries useful in assay systems. These systems include automatedworkstations including an automated synthesis apparatus and roboticsystems utilizing robotic arms. Any of the above devices are suitablefor use with the present invention, e.g., for high-throughput screeningof potential modulators. The nature and implementation of modificationsto these devices (if any) so that they can operate as discussed hereinwill be apparent to persons skilled in the relevant art.

Indeed, entire high throughput screening systems are commerciallyavailable. These systems typically automate entire procedures includingall sample and reagent pipetting, liquid dispensing, timed incubations,and final readings of the microplate in detector(s) appropriate for theassay. These configurable systems provide high throughput and rapidstart up as well as a high degree of flexibility and customization.Similarly, microfluidic implementations of screening are alsocommercially available.

The manufacturers of such systems provide detailed protocols the varioushigh throughput. Thus, for example, Zymark Corp. provides technicalbulletins describing screening systems for detecting the modulation ofgene transcription, ligand binding, and the like. The integrated systemsherein, in addition to providing for sequence alignment and, optionally,synthesis of relevant nucleic acids, can include such screeningapparatus to identify modulators that have an effect on one or morepolynucleotides or polypeptides according to the present invention.

In some assays it is desirable to have positive controls to ensure thatthe components of the assays are working properly. At least two types ofpositive controls are appropriate. That is, known transcriptionalactivators or inhibitors can be incubated with cells/plants/etc. in onesample of the assay, and the resulting increase/decrease intranscription can be detected by measuring the resulting increase inRNA/protein expression, etc., according to the methods herein. It willbe appreciated that modulators can also be combined with transcriptionalactivators or inhibitors to find modulators that inhibit transcriptionalactivation or transcriptional repression. Either expression of thenucleic acids and proteins herein or any additional nucleic acids orproteins activated by the nucleic acids or proteins herein, or both, canbe monitored.

In an embodiment, the invention provides a method for identifyingcompositions that modulate the activity or expression of apolynucleotide or polypeptide of the invention. For example, a testcompound, whether a small or large molecule, is placed in contact with acell, plant (or plant tissue or explant), or composition comprising thepolynucleotide or polypeptide of interest and a resulting effect on thecell, plant, (or tissue or explant) or composition is evaluated bymonitoring, either directly or indirectly, one or more of: expressionlevel of the polynucleotide or polypeptide, activity (or modulation ofthe activity) of the polynucleotide or polypeptide. In some cases, analteration in a plant phenotype can be detected following contact of aplant (or plant cell, or tissue or explant) with the putative modulator,e.g., by modulation of expression or activity of a polynucleotide orpolypeptide of the invention. Modulation of expression or activity of apolynucleotide or polypeptide of the invention may also be caused bymolecular elements in a signal transduction second messenger pathway andsuch modulation can affect similar elements in the same or anothersignal transduction second messenger pathway.

XIV. SUBSEQUENCES

Also contemplated are uses of polynucleotides, also referred to hereinas oligonucleotides, typically having at least 12 bases, preferably atleast 15, more preferably at least 20, 30, or 50 bases, which hybridizeunder at least highly stringent (or ultra-high stringent orultra-ultra-high stringent conditions) conditions to a polynucleotidesequence described above. The polynucleotides may be used as probes,primers, sense and antisense agents, and the like, according to methodsas noted supra.

Subsequences of the polynucleotides of the invention, includingpolynucleotide fragments and oligonucleotides are useful as nucleic acidprobes and primers. An oligonucleotide suitable for use as a probe orprimer is at least about 15 nucleotides in length, more often at leastabout 18 nucleotides, often at least about 21 nucleotides, frequently atleast about 30 nucleotides, or about 40 nucleotides, or more in length.A nucleic acid probe is useful in hybridization protocols, e.g., toidentify additional polypeptide homologues of the invention, includingprotocols for microarray experiments. Primers can be annealed to acomplementary target DNA strand by nucleic acid hybridization to form ahybrid between the primer and the target DNA strand, and then extendedalong the target DNA strand by a DNA polymerase enzyme. Primer pairs canbe used for amplification of a nucleic acid sequence, e.g., by thepolymerase chain reaction (PCR) or other nucleic-acid amplificationmethods. See Sambrook and Ausubel, supra.

In addition, the invention includes an isolated or recombinantpolypeptide including a subsequence of at least about 15 contiguousamino acids encoded by the recombinant or isolated polynucleotides ofthe invention. For example, such polypeptides, or domains or fragmentsthereof, can be used as immunogens, e.g., to produce antibodies specificfor the polypeptide sequence, or as probes for detecting a sequence ofinterest. A subsequence can range in size from about 15 amino acids inlength up to and including the full length of the polypeptide.

To be encompassed by the present invention, an expressed polypeptidewhich comprises such a polypeptide subsequence performs at least onebiological function of the intact polypeptide in substantially the samemanner, or to a similar extent, as does the intact polypeptide. Forexample, a polypeptide fragment can comprise a recognizable structuralmotif or functional domain such as a DNA binding domain that binds to aspecific DNA promoter region, an activation domain or a domain forprotein-protein interactions.

XV. PRODUCTION OF TRANSGENIC PLANTS Modification of Traits

The polynucleotides of the invention are favorably employed to producetransgenic plants with various traits, or characteristics, that havebeen modified in a desirable manner, e.g., to improve the seedcharacteristics of a plant. For example, alteration of expression levelsor patterns (e.g., spatial or temporal expression patterns) of one ormore of the transcription factors (or transcription factor homologues)of the invention, as compared with the levels of the same protein foundin a wild type plant, can be used to modify a plant's traits. Anillustrative example of trait modification, improved characteristics, byaltering expression levels of a particular transcription factor isdescribed further in the Examples and the Sequence Listing.

Arabidopsis as a Model System

Arabidopsis thaliana is the object of rapidly growing attention as amodel for genetics and metabolism in plants. Arabidopsis has a smallgenome, and well documented studies are available. It is easy to grow inlarge numbers and mutants defining important genetically controlledmechanisms are either available, or can readily be obtained. Variousmethods to introduce and express isolated homologous genes are available(see Koncz, et al., eds. Methods in Arabidopsis Research. et al. (1992),World Scientific, New Jersey, New Jersey, in “Preface”). Because of itssmall size, short life cycle, obligate autogamy and high fertility,Arabidopsis is also a choice organism for the isolation of mutants andstudies in morphogenetic and development pathways, and control of thesepathways by transcription factors (Koncz, supra, p. 72). A number ofstudies introducing transcription factors into A. thaliana havedemonstrated the utility of this plant for understanding the mechanismsof gene regulation and trait alteration in plants. See, for example,Koncz, supra, and U.S. Pat. No. 6,417,428).

Arabidopsis Genes in Transgenic Plants.

Expression of genes which encode transcription factors modify expressionof endogenous genes, polynucleotides, and proteins are well known in theart. In addition, transgenic plants comprising isolated polynucleotidesencoding transcription factors may also modify expression of endogenousgenes, polynucleotides, and proteins. Examples include Peng et al.(1997, Genes and Development 11:3194-3205) and Peng et al. (1999,Nature, 400:256-261). In addition, many others have demonstrated that anArabidopsis transcription factor expressed in an exogenous plant specieselicits the same or very similar phenotypic response. See, for example,Fu et al. (2001, Plant Cell 13:1791-1802); Nandi et al. (2000, Curr.Biol. 10:215-218); Coupland (1995, Nature 377:482-483); and Weigel andNilsson (1995, Nature 377:482-500).

Homologous Genes Introduced into Transgenic Plants.

Homologous genes that may be derived from any plant, or from any sourcewhether natural, synthetic, semi-synthetic or recombinant, and thatshare significant sequence identity or similarity to those provided bythe present invention, may be introduced into plants, for example, cropplants, to confer desirable or improved traits. Examples ofnon-arabidopsis sequences homologous to arabidopsis are listed in Table4. Consequently, transgenic plants may be produced that comprise arecombinant expression vector or cassette with a promoter operablylinked to one or more sequences homologous to presently disclosedsequences. The promoter may be, for example, a plant or viral promoter.

TABLE 4 Orthologs of arabidopsis sequences Smallest Test Sequence SEQ IDTest Sum Test Sequence GenBank NO GID Sequence ID Probability SpeciesAnnotation 859 G192 AW596933 7.70E-40 [Glycine max] sj84f07.yl Gm-c1034Glycine max cDNA clone GENO 859 G192 AV423663 2.40E-39 [Lotus japonicus]AV423663 Lotus japonicus young plants (two- 859 G192 B1422074 4.50E-34[Lycopersicon esculentum] EST532740 tomato callus, TAMU Lycop 859 G192AW447931 1.40E-27 [Triticum aestivum] BRY_1082 BRY Triticum aestivumcDNA clone 859 G192 BE998060 2.60E-24 [Medicago truncatula] EST429783GVSN Medicago truncatula cDNA 859 G192 AC018727 1.70E-23 [Oryza sativa]chromosome 10 clone OSJNBa0056G17,*** SEQUENC 859 G192 BG600477 1.00E-20[Solanum tuberosum] EST505372 cSTS Solanum tuberosum cDNA clo 859 G192BG356878 2.80E-16 [Sorghum bicolor] OV2_11_B04.g1_A002 Ovary 2 (OV2)Sorghum bi 859 G192 gi12039364 1.10E-31 [Oryza sativa] putativeDNA-binding protein. 859 G192 gi4894963 3.30E-14 [Avena sativa]DNA-binding protein WRKY3. 859 G192 gi1432056 5.80E-14 [Petroselinumcrispum] WRKY3. 859 G192 gi4760596 2.60E-13 [Nicotiana tabacum]DNA-binding protein NtWRKY3. 859 G192 gi11993901 1.40E-12 [Dactylisglomerata] somatic embryogenesis related protein. 859 G192 gi9270257.60E-09 [Cucumis sativus] SPF 1-like DNA-binding protein. 859 G192gi13620227 8.40E-09 [Lycopersicon esculentum] hypothetical protein. 859G192 gi3420906 2.80E-08 [Pimpinella brachycarpa] zinc finger protein;WRKY1. 859 G192 gi1159877 4.70E-08 [Avena fatua] DNA-binding protein.859 G192 gi484261 1.60E-07 [Ipomoea batatas] SPF1 protein. 801 G1946LPHSF8 1.10E-119 [Lycopersicon peruvianum] L.peruvianum Lp-hsf8 mRNA forheat 801 G1946 AC087771 4.10E-112 [Medicago truncatula] clone 8D15,***SEQUENCING IN PROGRESS 801 G1946 LEHSF8 5.90E-103 [Lycopersiconesculentum] L.esculentum Le-hsf8 gene for heat 801 G1946 AW5691383.10E-75 [Glycine max] si63g09.yl Gm-r1030 Glycine max cDNA clone GENO801 G1946 BG890899 1.30E-70 [Solanum tuberosum] EST516750 cSTD Solanumtuberosum cDNA clo 801 G1946 AC027658 4.60E-53 [Oryza sativa] subsp.japonica BAC nbxb0006I13, chromosome 10 801 G1946 AV833112 4.90E-52[Hordeum vulgare subsp.vulgare] AV833112 K. Sato unpublished 801 G1946gi19492 2.80E-121 [Lycopersicon peruvianum] heat shock transcriptionfactor 8 801 G1946 gi19260 5.10E-106 [Lycopersicon esculentum] heatstress transcription factor 801 G1946 gi662924 2.00E-47 [Glycine max]heat shock transcription factor 21. 801 G1946 gi5821138 9.70E-46[Nicotiana tabacum] heat shock factor. 801 G1946 gi11761077 2.90E-40[Oryza sativa] putative heat shock factor protein 1 (HSF 1) 801 G1946gi886742 3.20E-40 [Zea mays] heat shock factor. 801 G1946 gi71588822.70E-38 [Medicago sativa] heat shock transcription factor. 801 G1946gi3550588 1.90E-30 [Pisum sativum] heat shock transcription factor(HSFA). 801 G1946 gi100546 0.46 [Avena sativa] avenin precursor - oat.801 G1946 gi14190783 1 [Apium graveolens] putative phloem transcriptionfactor M1. 239 G375 AW696439 3.40E-33 [Medicago truncatula]NF106B07ST1F1060 Developing stem Medica 239 G375 BG595870 1.90E-31[Solanum tuberosum] EST494548 cSTS Solanum tuberosum cDNA clo 239 G375A1899263 3.70E-31 [Lycopersicon esculentum] EST268706 tomato ovary, TAMULycope 239 G375 NTBBF3 4.00E-31 [Nicotiana tabacum] N.tabacum mRNA forzinc finger protein, B 239 G375 BG405482 2.70E-30 [Glycine max]sac44a11.y1 Gm-c1062 Glycine max cDNA clone GEN 239 G375 AB0281303.30E-30 [Oryza sativa] mRNA for Dof zinc finger protein, complete cds239 G375 AB026297 7.30E-28 [Pisum sativum] mRNA for elicitor-responsiveDof protein ERDP 239 G375 HVBPBF 1.10E-27 [Hordeum vulgare] mRNA for DNAbinding protein BPBF. 239 G375 BG263089 1.70E-27 [Triticum aestivum]WHE2337_A02 A03ZS Wheat pre-anthesis spik 239 G375 ZMU82230 4.20E-27[Zea mays] endosperm-specific prolamin box binding factor (PB 239 G375gi4996640 1.90E-37 [Oryza sativa] Dof zinc finger protein. 239 G375gi3777436 8.10E-35 [Hordeum vulgare] DNA binding protein. 239 G375gi2393775 1.10E-33 [Zea mays] prolamin box binding factor. 239 G375gi1360088 2.00E-33 [Nicotiana tabacum] Zn finger protein. 239 G375gi3790264 4.30E-32 [Triticum aestivum] PBF protein. 239 G375 gi60920161.30E-29 [Pisum sativum] elicitor-responsive Dof protein ERDP. 239 G375gi7688355 5.60E-29 [Solanum tuberosum] Dof zinc finger protein. 239 G375gi1669341 4.60E-20 [Cucurbita maxima] AOBP (ascorbate oxidasepromoter-binding 239 G375 gi3929325 5.50E-18 [Dendrobium grex MadameThong-In] putative DNA-binding prot 239 G375 gi19547 5.50E-06 [Medicagosativa subsp. falcata] environmental stress and a 273 G1255 AC0871811.60E-46 [Oryza sativa] chromosome 3 clone OSJNBa0018H01, *** SEQUENCI273 G1255 BG239774 4.50E-33 [Glycine max] clone GEN 273 G1255 BG3213361.70E-32 [Descurainia sophia] Ds01_06h10_A DsO1_AAFC ECORC_cold_stress273 G1255 A1772841 2.90E-30 [Lycopersicon esculentum] E5T253941 tomatoresistant, Cornell 273 G1255 BF480245 4.60E-29 [Mesembryanthem umcrystallinum] L0-2152T3 Ice plant Lambda Un 273 G1255 AW688119 2.10E-28[Medicago truncatula] NF002E075T1F1000 Developing stem Medica 273 G1255BF266327 1.80E-26 [Hordeum vulgare] HV_CEa00l4N02fHordeum vulgareseedling gre 273 G1255 AW671538 5.80E-25 [Sorghum bicolor]LG1_348_B08.bl_A002_Light Grown 1 (LG1)Sor 273 G1255 B1072021 5.30E-20[Populus tremula x C067P76U Populus stra Populus tremuloides] 273 G1255BG273908 4.90E-19 [Vitis vinifera] EST 110 Green Grape berries LambdaZap II Li 273 G1255 gi13702811 3.70E-52 [Oryza sativa] putative zincfinger protein. 273 G1255 gi11037311 4.00E-21 [Brassica nigra]constans-like protein. 273 G1255 gi2303683 1.10E-19 [Brassica napus]unnamed protein product. 273 G1255 gi4091804 2.30E-18 [Malus xdomestica] CONSTANS-like protein 1. 273 G1255 gi3341723 4.30E-18[Raphanus sativus] CONSTANS-like 1 protein. 273 G1255 gi109463375.20E-17 [Ipomoea nil] CONSTANS-like protein. 273 G1255 gi45570933.30E-15 [Pinus radiata] zinc finger protein. 273 G1255 gi8132543 0.97[Chloroplast Zamia furfuracea] cytochrome b559 alpha subuni 273 G1255gi11795 0.99 [Nicotiana tabacum] put. psbE protein (aa 1-83). 273 G1255gi65646 0.99 [Chloroplast Nicotiana tabacum] cytochrome b559 component p557 G865 BE419451 3.70E-32 [Triticum aestivum] WWS012.C2R000101 ITEC WWSWheat Scutellum 557 G865 AW560968 1.10E-28 [Medicago truncatula]EST316016 DSIR Medicago truncatula cDNA 557 G865 AW782252 1.20E-26[Glycine max] sm03d11.y1 Gm-c1027 Glycine max cDNA clone GENO 557 G865B1421895 3.60E-25 [Lycopersicon esculentum] E5T532561 tomato callus,TAMU Lycop 557 G865 BE642320 1.60E-24 [Ceratopteris richardii]Cri2_5_L17_SP6 Ceratopteris Spore Li 557 G865 BE494041 1.60E-24 [Secalecereale] WHE1277_B09_D17ZS Secale cereale anther cDNA 557 G865 D399142.60E-24 [Oryza sativa] RJCS1576A Rice shoot Oryza sativa cDNA, mRNA s557 G865 AV428124 9.00E-23 [Lotus japonicus] AV428124 Lotus japonicusyoung plants (two- 557 G865 TOBBY4D 1.80E-21 [Nicotiana tabacum] TobaccomRNA for EREBP-2, complete cds. 557 G865 gi1208495 2.40E-23 [Nicotianatabacum] ERF1. 557 G865 gi8809571 5.10E-23 [Nicotiana sylvestris]ethylene-responsive element binding 557 G865 gi3342211 1.40E-22[Lycopersicon esculentum] Pti4. 557 G865 gi7528276 1.70E-22[Mesembryanthem um crystallinum] AP2-related transcription f 557 G865gi15217291 7.80E-22 [Oryza sativa] Putative AP2 domain containingprotein. 557 G865 gi3264767 2.70E-21 [Prunus armeniaca] AP2 domaincontaining protein. 557 G865 gi8980313 2.10E-20 [Catharanthus roseus]AP2-domain DNA-binding protein. 557 G865 gi8571476 9.30E-20 [Atriplexhortensis] apetala2 domain-containing protein. 557 G865 gi16882331.40E-19 [Solanum tuberosum] DNA binding protein homolog. 557 G865gi6478845 1.80E-19 [Matricaria chamomilla] ethylene-responsive elementbinding 23 G2509 BH577856 2.50E-29 [Brassica oleracea] BOHOJ67TR BOHOBrassica oleracea genomic 23 G2509 BM269574 5.90E-28 [Glycine max]sak01eO8.yl Gm-c1074 Glycine max cDNA clone SOY 23 G2509 BE4194512.20E-27 [Triticum aestivum] WWS012.C2R000101 ITEC WWS Wheat Scutellum23 G2509 A1483636 7.80E-27 [Lycopersicon esculentum] E5T249507 tomatoovary, TAMU Lycope 23 G2509 AW560968 8.90E-27 [Medicago truncatula]EST316016 DSIR Medicago truncatula cDNA 23 G2509 BE642320 4.30E-26[Ceratopteris richardii] Cri2_S_L17_SP6 Ceratopteris Spore Li 23 G2509AP003286 1.00E-25 [Oryza sativa] chromosome 1 clone P0677H08, ***SEQUENCING IN 23 G2509 BE494041 3.20E-25 [Secale cereale]WHE1277_B09_D17ZS Secale cereale anther cDNA 23 G2509 BE602106 1.10E-24[Hordeum vulgare] HVSMEh0102I06f Hordeum vulgare 5-45 DAP spi 23 G2509AV428124 1.00E-23 [Lotus japonicus] AV428124 Lotus japonicus youngplants (two- 23 G2509 gi3264767 4.00E-27 [Prunus armeniaca] AP2 domaincontaining protein. 23 G2509 gi12003376 1.40E-23 [Nicotiana tabacum]Avr9/Cf-9 rapidly elicited protein 1. 23 G2509 gi14140141 2.30E-23[Oryza sativa] putative AP2-related transcription factor. 23 G2509gi1688233 5.40E-23 [Solanum tuberosum] DNA binding protein homolog. 23G2509 gi4099921 2.60E-22 [Stylosanthes hamata] EREBP-3 homolog. 23 G2509gi8809571 7.80E-22 [Nicotiana sylvestris] ethylene-responsive elementbinding 23 G2509 gi3342211 1.00E-21 [Lycopersicon esculentum] Pti4. 23G2509 gi7528276 2.70E-21 [Mesembryanthemum crystallinum] AP2-relatedtranscription f 23 G2509 gi17385636 1.90E-20 [Matricaria chamomilla]ethylene-responsive element binding 23 G2509 gi1849606 3.30E-20 [Fagussylvatica] ethylene responsive element binding prote 1119 G2347 B19315175.30E-31 [Lycopersicon esculentum] E5T551406 tomato flower, 8 mm to pr1119 G2347 BE058432 4.20E-29 [Glycine max] sn16a06.yl Gm-c1016 Glycinemax eDNA clone GENO 1119 G2347 AMSPB1 1.80E-28 [Antirrhinum majus]A.majus mRNA for squamosa-promoter bindin 1119 G2347 BG525285 5.70E-28[Stevia rebaudiana] 48-3 Stevia field grown leaf cDNA Stevia 1119 G2347L38193 4.60E-27 [Brassica rapa] BNAF1025E Mustard flower buds Brassicarapa c 1119 G2347 BG455868 6.40E-27 [Medicago truncatula]NF068F05PL1F1045 Phosphate starved leaf 1119 G2347 BG097153 1.70E-24[Solanum tuberosum] E5T461672 potato leaves and petioles Sola 1119 G2347BF482644 1.60E-23 [Triticum aestivum] WHE2301-2304_A21_A21ZS Wheatpre-anthesis 1119 G2347 AW747167 2.30E-23 [Sorghum bicolor]WS1_66_F11.b1_A002 Water-stressed 1 (WS1) S 1119 G2347 BG442540 2.50E-23[Gossypium arboreum] GA_Ea0017G06f Gossypium arboreum 7-10 d 1119 G2347gi1183864 1.50E-31 [Antirrhinum majus] squamosa-promoter binding protein2. 1119 G2347 gi5931786 3.40E-25 [Zea mays] SBP-domain protein 5. 1119G2347 gi8468036 1.40E-21 [Oryza sativa] Similar to Arabidopsis thalianachromosome 2 1119 G2347 gi9087308 6.60E-09 [Mitochondrion Beta vulgarisorf102a. var. altissima] 1119 G2347 gi7209500 0.83 [Brassica rapa]S-locus pollen protein. 43 G988 CRU303349 3.10E-208 [Capsella rubella]ORF1, ORF2, ORF3, ORF4, ORF5 and ORF6(pa 43 G988 A84072 4.50E-86[Lycopersicon esculentum] Sequence 1 from Patent WO9846759. 43 G988A84080 3.30E-85 [Solanum tuberosum] Sequence 9 from Patent WO9846759. 43G988 AP003944 1.30E-57 [Oryza sativa] chromosome 6 clone OJ1126_F05, ***SEQUENCING 43 G988 AX081276 2.80E-43 [Brassica napus] Sequence 1 fromPatent WO0109356. 43 G988 ZMA242530 1.50E-40 [Zea mays] partial d8 genefor gibberellin response modulato 43 G988 AX005804 2.50E-37 [Triticumaestivum] Sequence 13 from Patent WO9909174. 43 G988 AB048713 9.10E-33[Pisum sativum] PsSCR mRNA for SCARECROW, complete cds. 43 G988 AW7745152.00E-29 [Medicago truncatula] E5T333666 KV3 Medicago truncatula cDNA 43G988 BE822458 1.20E-27 [Glycine max] GM700017A20H12 Gm-r1070 Glycine maxcDNA clone 43 G988 gi13620166 8.00E-211 [Capsella rubella] hypotheticalprotein. 43 G988 gi4160441 1.40E-87 [Lycopersicon esculentum] lateralsuppressor protein. 43 G988 gi10178637 2.20E-48 [Zea mays] SCARECROW. 43G988 gi6970472 1.20E-47 [Oryza sativa] OsGAI. 43 G988 gi5640157 2.80E-45[Triticum aestivum] gibberellin response modulator. 43 G988 gi131701267.10E-45 [Brassica napus] unnamed protein product. 43 G988 gi133656101.10E-40 [Pisum sativum] SCARECROW. 43 G988 gi14318115 1.10E-14 [Zeamays subsp. mays] gibberellin response modulator. 43 G988 gi143181657.30E-14 [Tripsacum dactyloides] gibberellin response modulator. 43 G988gi347457 2.40E-05 [Glycine max] hydroxyproline-rich glycoprotein. 459G2346 AMA011622 3.10E-35 [Antirrhinum majus] mRNA for squamosa promoterbinding 459 G2346 AW691786 1.80E-26 [Medicago truncatula]NF044B06ST1F1000 Developing stem Medica 459 G2346 AQ273505 7.00E-25[Oryza sativa] nbxb0030O03f CUGI Rice BAC Library Oryza sativ 459 G2346AW932595 7.90E-24 [Lycopersicon esculentum] EST358438 tomato fruitmature green 459 G2346 BG593787 9.50E-24 [Solanum tuberosum] EST492465cSTS Solanum tuberosum cDNA clo 459 G2346 BG442540 1.00E-23 [Gossypiumarboreum] GA__Ea00l7G06fGossypium arboreum 7-10 d 459 G2346 A79190341.90E-23 [Zea mays] 1006013G02.x3 1006 - RescueMu GridGZea mays geno 459G2346 B596165 2.70E-23 [Sorghum bicolor] PI1_50_D04.b1_(—) A002 Pathogeninduced 1 (PI1) 459 G2346 A1443033 2.30E-22 [Glycine max] sa31a08.ylGm-c1004 Glycine max cDNA clone GENO 459 G2346 BF482644 4.30E-22[Triticum aestivum] WHE2301-2304_A21_A21ZS Wheat pre-anthesis 459 G2346gi5931643 6.20E-45 [Antirrhinum majus] squamosa promoter bindingprotein-homol 459 G2346 gi5931786 4.20E-26 [Zea mays] SBP-domain protein5. 459 G2346 gi8468036 3.30E-14 [Oryza sativa] Similar to Arabidopsisthaliana chromosome 2 459 G2346 gi9087308 8.30E-08 [Mitochondrion Betavilgaris var. altissima] orf102a. 285 G1354 BG128374 2.90E-58[Lycopersicon esculentum] E5T474020 tomato shoot/meristem Lyc 285 G1354BE202831 1.90E-56 [Medicago truncatula] E5T402853 KV1 Medicagotruncatula cDNA 285 G1354 A1161918 6.60E-55 [Populus tremula x Populustremuloides] A009P50U Hybrid aspen 285 G1354 AB028186 1.20E-53 [Oryzasativa] mRNA for OsNAC7 protein, complete cds. 285 G1354 BE0609218.00E-50 [Hordeum vulgare] HVSMEg0013N15f Hordeum vulgare pre-anthesis285 G1354 AF402603 1.50E-42 [Phaseolus vulgaris] NAC domain protein NAC2mRNA, complete c 285 G1354 BE357920 1.60E-42 [Sorghum bicolor]DG1_23_F03.b1_A002 Dark Grown 1 (DG1) Sorgh 285 G1354 PHRNANAM 3.60E-42[Petunia x hybrida] P.hybrida mRNA encoding NAM protein. 285 G1354AW185617 5.30E-40 [Glycine max] se80b05.y1 Gm-c 1023Glycine max cDNAclone GENO 285 G1354 gi6006373 4.50E-63 [Oryza sativa] Similar to NAMlike protein (AC005310). 285 G1354 gi5148914 2.30E-44 [Phaseolusvulgaris] NAC domain protein NAC2. 285 G1354 gi14485513 3.50E-44[Solanum tuberosum] putative NAC domain protein. 285 G1354 gi12796405.90E-44 [Petunia x hybrida] NAM. 285 G1354 gi6175246 5.20E-41[Lycopersicon esculentum] jasmonic acid 2. 285 G1354 gi4218535 5.10E-39[Triticum sp.] GRAB1 protein. 285 G1354 gi6732158 5.10E-39 [Triticummonococcum] unnamed protein product. 285 G1354 gi7716952 3.30E-35[Medicago truncatula] NACi. 285 G1354 gi4996349 2.50E-26 [Nicotianatabacum] NAC-domain protein. 285 G1354 gi2982275 3.10E-14 [Piceamariana] ATAF1-like protein. 119 G1063 BH700922 4.50E-90 [Brassicaoleracea] BOMMZ07TR BO_2_3_KB Brassica oleraceagen 119 G1063 BE4511742.40E-41 [Lycopersicon esculentum] E5T402062 tomato root, plants pre-a119 G1063 AW832545 2.00E-40 [Glycine max] sm12e10.y1 Gm-c1027 Glycinemax cDNA clone GENO 119 G1063 AP004693 5.90E-37 [Oryza sativa]chromosome 8 clone P0461F06 *** SEQUENCING IN 119 G1063 AP0044624.40E-32 [Oryza sativa (japonica ( ) chromosome 8 clo cultivar-group)]119 G1063 AT002234 8.90E-32 [Brassica rapa subsp.pekinensis] AT002234Flower bud cDNA Br 119 G1063 BF263465 5.40E-25 [Hordeum vulgare]HV_CEa0006N02f Hordeum vulgare seedling gre 119 G1063 BG557011 4.20E-22[Sorghum bicolor] EM1_41_E02.gl_A002 Embryo 1 (EM1) Sorghum b 119 G1063BG842856 3.10E-21 [Zea mays] MEST40-H05.T3 ISUM4-TN Zea mays cDNA cloneMEST40- 119 G1063 BG559930 1.40E-18 [Sorghum propinquum]RHIZ2_75_D09.gl_A003 Rhizome2 (RHIZ2) So 119 G1063 gi15528743 4.20E-26[Oryza sativa] contains EST C74560(E31855)~unknown protein. 119 G1063gi6166283 8.10E-10 [Pinus taeda] helix-loop-helix protein lA. 119 G1063gi11045087 8.80E-09 [Brassica napus] putative protein. 119 G1063gi10998404 7.10E-08 [Petunia x hybrida] anthocyanin 1. 119 G1063 gi994412.60E-07 [Volvox carteri] sulfated surface glycoprotein 185 - Volvox 119G1063 gi1142621 5.00E-07 [Phaseolus vulgaris] phaseolin G-box bindingprotein PG2. 119 G1063 gi166428 8.10E-07 [Antirrhinum majus] DEL. 119G1063 gi1247386 9.50E-07 [Nicotiana alata] PRP2. 119 G1063 gi820911.00E-06 [Lycopersicon esculentum] hydroxyproline-rich glycoprotein 119G1063 gi1486263 1.40E-06 [Catharanthus roseus] extensin. 129 G2143BH650724 3.00E-88 [Brassica oleracea] BOMIW43TR BO_2_3_KB Brassicaoleracea gen 129 G2143 AW832545 1.50E-40 [Glycine max] sm12e10.y1Gm-c1027 Glycine max cDNA clone GENO 129 G2143 BE451174 3.50E-40[Lycopersicon esculentum] E5T402062 tomato root, plants pre-a 129 G2143AP004693 4.00E-38 [Oryza sativa] chromosome 8 clone P0461F06, ***SEQUENCING IN 129 G2143 AP004584 6.30E-33 [Oryza sativa(japonicacultivar-group)] ( )chromosome 8 clo 129 G2143 AT002234 3.00E-31[Brassica rapa subsp. pekinensis] AT002234 Flower bud cDNA Br 129 G2143BF263465 2.90E-26 [Hordeum vulgare] HV_CEa0006N02fHordeum vulgareseedling gre 129 G2143 BG557011 2.60E-22 [Sorghum bicolor]EM1_41_E02.g1_A002 Embryo 1 (EM1) Sorghum b 129 G2143 BG842856 3.50E-20[Zea mays] MEST4O-H05.T3 ISUM4-TN Zea mays cDNA clone MEST4O- 129 G2143BG559930 6.10E-18 [Sorghum propinquum] RHIZ2_75_D09.g1_A003 Rhizome2(RHIZ2) So 129 G2143 gi15528743 5.50E-26 [Oryza sativa] contains ESTC74560(E31855)~unknown protein. 129 G2143 gi1086538 7.60E-09 [Oryzarufipogon] transcriptional activator Rb homolog. 129 G2143 gi61662831.10E-08 [Pinus taeda] helix-loop-helix protein 1A. 129 G2143 gi11426214.60E-07 [Phaseolus vulgaris] phaseolin G-box binding protein PG2. 129G2143 gi3399777 5.20E-07 [Glycine max] symbiotic ammonium transporter;nodulin. 129 G2143 gi5923912 6.10E-07 [Tulipa gesneriana] bHLHtranscription factor GBOF-1. 129 G2143 gi10998404 9.20E-07 [Petunia xhybrida] anthocyanin 1. 129 G2143 gi4321762 5.20E-06 [Zea mays]transcription factor MYC7E. 129 G2143 gi166428 6.00E-06 [Antirrhinummajus] DEL. 129 G2143 gi527665 7.40E-06 [Sorghum bicolor] myc-likeregulatory R gene product. 133 G2557 BH511840 6.70E-62 [Brassicaoleracea] BOGRJ19TR BOGR Brassica oleracea genomic 133 G2557 BE3478113.70E-46 [Glycine max] sp05h10.y1 Gm-c1041 Glycine max cDNA clone GENO133 G2557 AP003141 2.40E-33 [Oryza sativa] genomic DNA, chromosome 1,PAC clone:P0002B05, 133 G2557 BF263465 3.00E-31 [Hordeum vulgare]HV_CEa0006N02fHordeum vulgare seedling gre 133 G2557 AT002234 6.60E-27[Brassica rapa subsp. pekinensis] AT002234 Flowerbud cDNA Br 133 G2557BG557011 6.40E-26 [Sorghum bicolor] EM1_41_E02.g1_A002 Embryo 1 (EM1)Sorghum b 133 G2557 AP004462 7.90E-26 [Oryza sativa ( )chromosome 8 clo(japonica cultivar-group)] 133 G2557 BE451174 3.90E-25 [Lycopersiconesculentum] E5T402062 tomato root, plants pre-a 133 G2557 BG8428565.60E-22 [Zea mays] MEST40-H05.T3 ISUM4-TN Zea mays cDNA clone MEST4O-133 G2557 BG559930 7.00E-14 [Sorghum propinquum] RH1Z2_75_D09.g1 A003Rhizome2 (RHIZ2) So 133 G2557 gi15289790 2.40E-36 [Oryza sativa]contains EST C74560(E31855)~unknown protein. 133 G2557 gi33997772.60E-06 [Glycine max] symbiotic ammonium transporter; nodulin. 133G2557 gi4206118 1.10E-05 [Mesembryanthemum crystallinum] transporterhomolog. 133 G2557 gi6166283 1.30E-05 [Pinus taeda] helix-loop-helixprotein 1A. 133 G2557 gi527655 3.70E-05 [Pennisetum glaucum] myc-likeregulatory R gene product. 133 G2557 gi5923912 3.70E-05 [Tulipagesneriana] bHLH transcription factor GBOF-1. 133 G2557 gi5276617.80E-05 [Phyllostachys acuta] myc-like regulatory R gene product. 133G2557 gi527665 9.50E-05 [Sorghum bicolor] myc-like regulatory R geneproduct. 133 G2557 gi1086538 0.0001 [Oryza rufipogon] transcriptionalactivator Rb homolog. 133 G2557 gi5669656 0.00013 [Lycopersiconesculentum] ER33 protein. 697 G2430 BF632520 1.90E-14 [Medicagotruncatula] NF039A08DT1F10541054 Drought Medicago trunc 697 G2430AW396912 1.20E-13 [Glycine max] sg64g09.y1 Gm-c1007 Glycine max cDNAclone GENO 697 G2430 D41804 4.50E-13 [Oryza sativa] RICS4626A Rice shootOryza sativa cDNA, mRNA s 697 G2430 BE214029 2.60E-10 [Hordeum vulgare]HV_CEb0001P06fHordeum vulgare seedling gre 697 G2430 AW564570 2.70E-10[Sorghum bicolor] LG1_296_E01.b1_A002 Light Grown 1 (LG1) Sor 697 G2430BG129795 5.40E-10 [Lycopersicon esculentum] EST475441 tomatoshoot/meristem Lyc 697 G2430 AB060130 5.40E-09 [Zea mays] ZmRR8 mRNA forresponse regulator 8, complete cds. 697 G2430 BF587105 2.50E-05 [Sorghumpropinquum] FM1_32_C0Sbi_A003 Floral-Induced Merist 697 G2430 AI1631210.3 [Populus tremula x Populus tremuloides] A033P70U Hybrid aspen 697G2430 BG595628 0.46 [Solanum tuberosum] EST494306 cSTS Solanum tuberosumcDNA clo 697 G2430 gi13661174 5.40E-18 [Zea mays] response regulator 8.697 G2430 gi15289981 0.028 [Oryza sativa] hypothetical protein. 697G2430 gi6942190 0.12 [Mesembryanthemum crystallinum] CDPK substrateprotein 1; C 697 G2430 gi4519671 0.2 [Nicotiana tabacum] transfactor.831 G1478 BF275913 1.50E-20 [Gossypium arboreum] GA__Eb0025C07fGossypiumarboreum 7-10 d 831 G1478 BG157399 6.50E-19 [Glycine max] sab36g12.y1Gm-c1026 Glycine max cDNA clone GEN 831 G1478 C95300 2.20E-10 [Citrusunshiu] C95300 Citrus unshiu Miyagawa-wase maturation 831 G1478 AW0345522.70E-10 [Lycopersicon esculentum] EST278168 tomato callus, TAMU Lycop831 G1478 B1070429 3.40E-10 [Populus tremula x Populus tremuloides]C037P68U Populus stra 831 G1478 AF016011 5.10E-09 [Brassica napus]CONSTANS homolog (Bn9C0N10) gene, complete c 831 G1478 BE598912 6.20E-09[Sorghum bicolor] P11_84_H11.bi_A002 Pathogen induced 1 (PI1) 831 G1478BG605313 6.80E-09 [Triticum aestivum] WHE2331_C04_F07ZS Wheatpre-anthesis spik 831 G1478 BE558327 8.90E-09 [Hordeum vulgare]HV_CEb0017Dl9fHordeum vulgare seedling gre 831 G1478 BG647091 1.20E-08[Medicago truncatula] EST508710 HOGA Medicago truncatula cDNA 831 G1478gi2895188 4.70E-11 [Brassica napus] CONSTANS homolog. 831 G1478gi3618308 1.50E-09 [Oryza sativa] zinc finger protein. 831 G1478gi11037308 4.70E-09 [Brassica nigra] constans-like protein 831 G1478gi3341723 1.30E-08 [Raphanus sativus] CONSTANS-like 1 protein. 831 G1478gi4091806 1.50E-07 [Malus x domestica] CONSTANS-like protein 2. 831G1478 gi10946337 3.10E-07 [Ipomoea nil] CONSTANS-like protein. 831 G1478gi4557093 1.40E-05 [Pinus radiata] zinc finger protein. 831 G1478gi619312 0.9 [Capparis masaikai] mabinlin III B-chain = sweet proteinmabi 831 G1478 gi4732091 1 [Zea mays] bundle sheath defective protein 2.831 G1478 gi4699629 1 [Nicotiana alata] Chain A, Putative AncestralProtein Encod 579 G681 BG128147 6.80E-41 [Lycopersicon esculentum]E5T473793 tomato shoot/meristem Lyc 579 G681 BF054497 1.50E-39 [Solanumtuberosum] E5T439727 potato leaves and petioles Sola 579 G681 BE0542768.40E-39 [Gossypium arboreum] GA__Ea0002018f Gossypium arboreum 7-10 d579 G681 BG269414 4.00E-38 [Mesembryanthemum L0-3478T3 Ice plant LambdaUn crystallinum] 579 G681 BF620286 7.40E-38 [Hordeum vulgare]HVSMEc0019F08f Hordeum vulgare seedling sho 579 G681 BE490032 1.00E-37[Triticum aestivum] WHE0364_C04_E08ZS Wheat cold-stressed see 579 G681B1542536 1.40E-36 [Zea mays] 949021A03.y1 949 - Juvenile leaf and shootcDNA fr 579 G681 BF425254 7.20E-36 [Glycine max] su42c10.y1 Gm-c1068Glycine max cDNA clone GENO 579 G681 AW672062 3.20E-34 [Sorghum bicolor]LG1_354_G05b1_A002 Light Grown 1 (LG1) Sor 579 G681 BG448527 1.00E-33[Medicago truncatula] NF036F04RT1F1032 Developing root Medica 579 G681gi13346188 9.10E-37 [Gossypium hirsutum] GHMYB25. 579 G681 gi205636.30E-36 [Petunia x hybrida] protein 1. 579 G681 gi485867 1.20E-34[Antirrhinum majus] mixta. 579 G681 gi2605617 1.70E-32 [Oryza sativa]OSMYB1. 579 G681 gi1430846 2.00E-31 [Lycopersicon esculentum]myb-related transcription factor. 579 G681 gi6651292 2.20E-30[Pimpinella brachycarpa] myb-related transcription factor. 579 G681gi15042116 4.90E-30 [Zea mays subsp. parviglumis] CI protein. 579 G681gi82730 6.10E-30 [Zea mays] transforming protein (myb) homolog (cloneZm38) 579 G681 gi5139806 8.30E-30 [Glycine max] GmMYB29A2. 579 G681gi19055 1.10E-29 [Hordeum vulgare] MybHv5. 611 G878 AF096299 6.20E-90[Nicotiana tabacum] DNA-binding protein 2 (WRKY2) mRNA, compl 611 G878CUSSLDB 1.80E-83 [Cucumis sativus] SPF 1-like DNA-binding protein mRNA,complet 611 G878 AF193802 3.50E-63 [Oryza sativa] zinc fingertranscription factor WRKY1 mRNA, c 611 G878 AX192162 2.20E-62 [Glycinemax] Sequence 9 from Patent WO0149840. 611 G878 IPBSPF1P 3.80E-58[Ipomoea batatas] Sweet potato mRNA for SPF1 protein, complet 611 G878AFABF1 2.00E-56 [Avena fatua] A.fatua mRNA for DNA-binding protein(cloneABF 611 G878 LE5303343 7.20E-55 [Lycopersicon esculentum] mRNA forhypothetical protein (ORF 611 G878 AX192164 4.00E-54 [Triticum aestivum]Sequence 11 from Patent WO0149840. 611 G878 AF080595 2.10E-53[Pimpinella brachycarpa] zinc finger protein (ZFP1) mRNA, com 611 G878PCU48831 2.30E-53 [Petroselinum crispum] DNA-binding protein WRKY1 mRNA,comple 611 G878 gi4322940 3.30E-128 [Nicotiana tabacum] DNA-bindingprotein 2. 611 G878 gi927025 1.10E-109 [Cucumis sativus] SPF1-likeDNA-binding protein. 611 G878 gi6689916 1.50E-74 [Oryza sativa] zincfinger transcription factor WRKY1 611 G878 gi484261 1.10E-66 [Ipomoeabatatas] SPF1 protein. 611 G878 gi1159877 2.30E-63 [Avena fatua]DNA-binding protein. 611 G878 gi13620227 4.60E-63 [Lycopersiconesculentum] hypothetical protein. 611 G878 gi5917653 1.70E-56[Petroselinum crispum] zinc-finger type transcription facto 611 G878gi4894965 5.00E-56 [Avena sativa] DNA-binding protein WRKY1. 611 G878gi3420906 8.70E-56 [Pimpinella brachycarpa] zinc finger protein; WRKY1.611 G878 gi13620168 4.20E-22 [Capsella rubella] hypothetical protein. 47G374 AP004457 1.20E-73 [Oryza sativa (japonica cultivar group)] ()chromosome 8 clo 47 G374 AP004693 1.90E-73 [Oryza sativa] chromosome 8clone P0461F06 *** SEQUENCING IN 47 G374 BH552835 1.30E-62 [Brassicaoleracea] BOHGT56TR BOHG Brassica oleracea genomic 47 G374 BG1282296.50E-55 [Lycopersicon esculentum] EST473875 tomato shoot/meristem Lyc47 G374 BG646959 3.20E-46 [Medicago truncatula] E5T508578 HOGA Medicagotruncatula cDNA 47 G374 BG890162 8.70E-41 [Solanum tuberosum] EST516013cSTD Solanum tuberosum cDNA clo 47 G374 AW179366 6.00E-38 [Zea mays]618046G06.y1 618 - Inbred Tassel cDNA Library Zea 47 G374 BF4732061.50E-32 [Triticum aestivum] WHE0922_G12_M24ZS Wheat 5-15 DAPspike cD 47G374 AW761011 2.90E-29 [Glycine max] s161g11.y1 Gm-c1027 Glycine maxcDNA clone GENO 47 G374 AJ436050 1.50E-27 [Hordeum vulgare] AJ436050S00007 Hordeum vulgare cDNA clone 47 G374 gi422012 0.8 [Sorghum bicolor]lipid transfer protein - sorghum (fragmen 47 G374 gi1827893 1 [Zea mays]Maize Nonspecific Lipid Transfer Protein Complex

The invention thus provides for methods for preparing transgenic plants,and for modifying plant traits. These methods include introducing into aplant a recombinant expression vector or cassette comprising afunctional promoter operably linked to one or more sequences homologousto presently disclosed sequences. Plants and kits for producing theseplants that result from the application of these methods are alsoencompassed by the present invention.

Traits of Interest

Examples of some of the traits that may be desirable in plants, and thatmay be provided by transforming the plants with the presently disclosedsequences, are listed in Table 5 and 6.

TABLE 5 Genes, traits, transcription factor families and conserveddomains Poly- Poly- nucleotide peptide SEQ GID SEQ ID Conserved ID NO:No. Trait Category Family Comment NO: domains 1 G1275 Architecture; Devand WRKY Reduced apical 2 (113-169) size morph dominance; small plant 3G1411 Architecture Dev and morph AP2 Loss of apical dominance 4 (87-154)5 G1488 Architecture; Dev and GATA/Zn Reduced apical 6 (221-246) lightmorph; seed dominance, shorter response; biochemistry stems;constitutive size; seed photomorphogenesis; protein reduced size;altered content seed protein content 7 G1499 Architecture; Dev andHLH/MYC Altered plant 8 (118-181) flower; morph architecture; alteredmorphology: floral organ identity other and development; dark greencolor 9 G1543 Architecture; Dev and HB Altered plant 10 (135-195)flower; morph; seed architecture; altered morphology: biochemistrycarpel shape; dark other; seed oil green color; decreased seed oil 11G1635 Architecture; Dev and MYB- Reduced apical 12 (44-104) morphology:morph related dominance; pale other; fertility green, smaller plants;reduced fertility 13 G1794 Architecture; Dev and AP2 Altered plant 14(182-248) light morph; seed architecture; response; biochemistryconstitutive seed oil and photomorphogenesis; protein content alteredseed oil and protein content 15 G1839 Architecture; Dev and AP2 Alteredplant 16 (118-184) size morph architecture; reduced size 17 G2108Architecture Dev and morph AP2 Altered inflorescence 18 (18-85)structure 19 G2291 Architecture; Dev and AP2 Altered plant 20 (TBD)flowering morph; architecture; late time flowering flowering time 21G2452 Architecture; Dev and MYB- Reduced apical 22 (27-213) leaf morphrelated dominance; pale green color 23 G2509 Architecture; Dev andmorph; AP2 Reduced apical 24 (89-156) seed oil and seed biochemistrydominance; altered protein content seed oil and protein content 25 G390Architecture Dev and HB Altered shoot 26 (18-81) morph development 27G391 Architecture Dev and HB Altered shoot 28 (25-85) morph development29 G438 Architecture; Dev and HB Reduced branching, 30 (22-85) stemmorph reduced lignin 31 G47 Architecture; Dev and morph; AP2 Alteredarchitecture 32 (11-80) stem; flowering and inflorescence floweringtime; seed development, structure time; altered biochemistry of vasculartissues; seed oil late flowering; altered content seed oil content 33G559 Architecture; Dev and bZIP Loss of apical 34 (203-264) fertilitymorph dominance; reduced fertility 35 G568 Architecture; Dev and bZIPAltered branching; late 36 (215-265) flowering morph; flowering timeflowering time 37 G580 Architecture; Dev and bZIP Alteredinflorescences; 38 (162-218) flower morph altered flower development 39G615 Architecture; Dev and TEO Altered plant 40 (88-147) fertility morpharchitecture; little or no pollen production, poor filament elongation41 G732 Architecture; Dev and bZIP Reduced apical 42 (31-91) flower;seed morph; seed dominance; abnormal oil and biochemistry flowers;altered seed protein oil and protein content content 43 G988Architecture; Dev and SCR Reduced lateral 44 (178-195) fertility; morph;seed branching; reduced flower; stem; biochemistry fertility; enlargedseed oil and floral organs, short protein pedicels; thicker stem,content altered distribution of vacular bundles; altered seed oil andprotein content 45 G1519 Embryo lethal Dev and morph RING/C3HC4 Embryolethal 46 (327-364) 47 G374 Embryo lethal Dev and morph Z-ZPF Embryolethal 48 (35-67, 245-277) 49 G877 Embryo lethal Dev and morph WRKYEmbryo lethal 50 (272-328, 487-603) 51 G1000 Fertility; size; Dev andMYB- Reduced fertility; 52 (14-117) flower; stem morph (R1)R2R3 smallplant; reduced or absent petals and sepals; reduced inflorescence, stemelongation 53 G1067 Fertility; leaf Dev and AT-hook Reduced fertility,54 (86-93) size morph altered leaf shape; small plant 55 G1075Fertility; flower; Dev and AT-hook Reduced fertility, 56 (78-85) leaf;size morph reduced or absent petals, sepals and stamens; altered leafshape; small plant 57 G1266 Fertility; size Dev and AP2 Reducedfertility; 58 (79-147) morph small plant 59 G1311 Fertility; size Devand MYB- Reduced fertility; 60 (11-112) morph (R1)R2R3 small plant 61G1321 Fertility; flower Dev and MYB- Poor fertility; altered 62 (4-106)morph (R1)R2R3 flower morphology 63 G1326 Fertility; flower; Dev andMYB- Reduced fertility; 64 (18-121) size morph (R1)R2R3 petals andsepals are smaller; small plant 65 G1367 Fertility; size Dev and AT-hookReduced fertility; 66 (179-201, morph reduced size 262-285, 298-319,335-357) 67 G1386 Fertility; size; Dev and AP2 Reduced fertility; 68(TBD) seed oil and morph; seed and reduced size; altered proteinbiochemistry seed oil and protein content content 69 G1421 Fertility;size; Dev and AP2 Reduced fertility; 70 (74-151) seed oil morph; seedsmall plant; altered content biochemistry seed oil content 71 G1453Fertility; Dev and NAC Reduced fertility; 72 (13-160) morphology: morphaltered inflorescence other development 73 G1560 Fertility; Dev and HSReduced fertility; 74 (62-151) flower; size morph altered flowerdevelopment; reduced size 75 G1594 Fertility; leaf; Dev and HB Reducedfertility; 76 (343-308) seed morph altered leaf shape and anddevelopment; large pale seed 77 G1750 Fertility; size Dev and AP2Reduced fertility; 78 (107-173) seed oil morph; seed reduced size;content biochemistry increased seed oil content 79 G1947 Fertility;flower; Dev and HS Reduced fertility; 80 (37-120) seed protein morph;seed and extended period of content biochemistry flowering; altered seedprotein content 81 G2011 Fertility; size Dev and HS Reduced fertility;82 (56-147) seed oil and morph; seed and reduced size; altered proteincontent biochemistry seed oil and protein content 83 G2094 Fertility;leaf; Dev and GATA/Zn Reduced fertility; 84 (43-68) size morph alteredleaf and development; reduced size 85 G2113 Fertility; leaf; Dev and AP2Reduced fertility; long 86 (TBD) seed protein morph; seed petioles,altered content biochemistry orientation; altered seed protein content87 G2115 Fertility; size Dev and morph AP2 Reduced fertility; 88(46-115) reduced size 89 G2130 Fertility; size; Dev and morph AP2Reduced fertility; 90 (93-160) senescence reduced size; early senescence91 G2147 Fertility; size Dev and morph HLM/MYC Reduced fertility; 92(160-234) reduced size 93 G2156 Fertility; size; Dev and morph; AT-hookReduced fertility; 94 (66-86) seed protein seed biochemistry reducedsize; altered content seed protein content 95 G2294 Fertility; size Devand morph AP2 Reduced fertility; 96 (32-102) reduced size 97 G2510Fertility; size Dev and morph AP2 Reduced fertility; 98 (41-108) reducedsize 99 G2893 Fertility; flower; Dev and morph MYB-(R1) Reducedfertility; 100 (19-120) size R2R3 altered flower development; reducedsize 101 G340 Fertility; size Dev and morph Z-C3H Reduced fertility,size 102 (37-154) 103 G39 Fertility; size Dev and morph AP2 Reducedfertility, 104 (24-90) small plant 105 G439 Fertility; size Dev andmorph AP2 Reduced fertility; 106 (110-177) small plant 107 G470Fertility Dev and morph ARF Short stamen filaments 108 (61-393) 109 G652Fertility; seed; Dev and morph; Z-CLDSH Reduced fertility; 110 (28-49,flower; size; seed biochemistry irregular shaped seed 137-151, seed oilcontent altered flower 182-196) development; reduced size, slow growth;altered seed oil content 111 G671 Fertility; flower; Dev and morphMYB-(R1) Reduced fertility; 112 (15-115) leaf size; stem R2R3abscission; altered leaf shape; small plant; altered inflorescence stemstructure 113 G779 Fertility; flower Dev and morph HLH/MYC Reducedfertility, 114 (126-182) homoerotic transformations 115 G962 Fertility;size Dev and morph NAC Reduced fertility; 116 (53-175) small plant 117G977 Fertility; leaf; Dev and morph AP2 Reduced fertility; 118 (5-72)morphology; other altered leaf shape; size dark green; small plant 119G1063 Flower; leaf; Dev and morph; HLM/MYC Altered flower 120 (131-182)inflorescence; seed biochemistry development, ectopic seed oil andcarpel tissue; altered protein content leaf shape, dark altered color;altered inflorescence development; altered seed oil and protein content121 G1140 Flower Dev and morph MADS Altered flower development 122(2-57) 123 G1425 Flower Dev and morph NAC Altered flower and 124(20-173) inflorescence 125 G1449 Flower Dev and morph IAA Altered flowerstructure 126 (48-53, 74-107, 122-152) 127 G1897 Flower; leaf; Dev andmorph Z-Dof Altered flower 128 (34-62) seed protein seed biochemistrydevelopment; content altered leaf development altered seed proteincontent 129 G2143 Flower; leaf; Dev and morph HLM/MYC Altered flower 130(128-179) inflorescence development, ectopic carpel tissue; altered leafshape, dark green color; altered inflorescence development 131 G2535Flower; seed Dev and morph; NAC Altered flower 132 (11-114) proteincontent seed biochemistry development; altered seed protein content 133G2557 Flower; leaf Dev and morph HLM/MYC Altered flower 134 (278-328)development ectopic carpel tissue; altered leaf shape, dark green color135 G259 Flower; leaf Dev and morph HS Altered flower 136 (27-131)development; altered leaf development 137 G353 Flower; leaf; size; Devand morph; Z-C2H2 Short pedicels, 138 (41-61, seed protein seedbiochemistry downward pointing 84-104) content siliques; altered leafdevelopment; reduced size; altered seed protein content 139 G354 Flower;light dev and morph Z-C2H2 Short pedicels, 140 (42-62 respond; sizedownward pointing 88-109) siliques; morphogenesis; reduced size 141 G638Flower; morphology: Dev and morph TH Altered flower 142 (119-206) otherdevelopment; multiple developmental defects 143 G869 Flower; morphology:Dev and morph; AP2 Abnormal anther 144 (109-177) other; seed oil seedbiochemistry development; small and spindly plant; altered seed fattyacids 145 G1645 Inflorescence; leaf Dev and morph MYB-(R1) Alteredinflorescence 146 (90-210) R2R3 structure; altered leaf development 147G1038 Leaf Dev and morph GARP Altered leaf shape 148 (198-247) 149 G1073Leaf; size; Dev and morph; AT-hook Serrated leaves; 150 (33-42,flowering time flowering time increased plant size; 18-175) floweringappears to be slightly delayed 151 G1146 Leaf Dev and morph PAZ Alteredleaf 152 (886-896) development 153 G1267 Leaf; size Dev and morph WRKYDark green shiny 154 (70-127) leaves; small plant 155 G1269 Leaf Dev andmorph MYB-related Long petioles, 156 (27-83) upturned leaves 157 G1452Leaf; trichome; Dev and morph; NAC Altered leaf shaped, 158 (30-177)flowering time flowering time dark green color; reduced trichomedensity; late flowering 159 G14949 Leaf; size; light Dev and morphHLH/MYC Pale green leaves, 160 (261-311) response; seed altered leafshape; reduced size; long hypocotyls; large, pale seeds 161 G1548 LeafDev and morph HB Altered leaf development 162 (17-77) 163 G1574 Leaf Devand morph SWI/SNF Altered leaf development 164 (28-350) 165 G1586 Leaf;size Dev and morph HB Narrow leaves; small 166 (21-81) plants 167 G1786Leaf; light Dev and morph MYB-(R1) Dark green, small 168 (TBD) response;size R2R3 leaves with short petioles; photo- photomorphogensis in thedark; small plant 169 G1792 Leaf; seed oil Dev and morph; AP2 Darkgreen, shiny 170 (17-85) and protein content seed biochemistry leaves;altered seed oil and protein content 171 G1865 Leaf; seed oil Dev andmorph; GRF-like Altered leaf 172 (124-149) and protein content seedbiochemistry development; altered seed oil and protein content 173 G1886Leaf; size Dev and morph Z-Dof Chlorotic patches in 174 (17-59) leaves;reduced size 175 G1933 Leaf; size; seed Dev and morph; WRKY Altered leaf176 (205-263, protein content seed biochemistry development; reducedsize 344-404) altered seed protein content 177 G2059 Leaf; seed oil Devand morph; AP2 Smaller, curled leaves; 178 (184-254) and protein contentseed altered seed oil, biochemistry protein content 179 G2105 Leaf; seedDev and morph TH Alteration in leaf 180 (100-153) surface; large, paleseeds 181 G2117 Leaf; seed oil Dev and morph; bZIP Small, dark green 182(46-106) and protein content seed biochemistry leaves; altered seed oiland protein content 183 G2124 Leaf; seed protein Dev and morph; TEOAltered leaf 184 (75-132) content seed development; altered biochemistryseed protein content 185 G2140 Leaf; root Dev and morph HLH/MYC Alteredleaf 186 (167-242) development; short roots 187 G2144 Leaf; lightresponse; Dev and morph HLH/MYC Pale green leaves, 188 (203-283) size;seed oil content seed altered leaf shape; biochemistry long hypocotyls;reduced size; altered seed oil content 189 G2431 Leaf Dev and morph GARPDark green leaves; 190 (38-88) reduced size 191 G2465 Morphology; other;Dev and morph GARP Slowed development; 192 (219-269) leaf altered leafcolor and shape 193 G2583 Leaf; seed oil Dev and morph AP2 Glossy, shinyleaves; 194 (4-71) and protein content seed biochemistry altered seedoil and protein content 195 G2724 Leaf Dev and morph MYB-(R1)R2R3 Darkgreen leaves 196 (7-113) 197 G377 Leaf; morphology: Dev and morphRING/C3H2C3 Altered leaf 198 (85-128) other development; slow growth 199G428 Leaf Dev and morph HB Altered leaf shape 200 (229-292) 201 G447Leaf; morphology: Dev and morph ARF Dark green leaves; 202 (22-356)other; size altered cotyledon shape; reduced size 203 G464 Leaf Dev andmorph IAA Altered leaf shape 204 (20-28, 71-82, 126-142, 187-224) 205G557 Leaf; size Dev and morph bZIP Dark green color; 206 (90-150) smallplant 207 G577 Leaf Dev and morph BZIPT2 Reduced size, 208 (TBD)increased anthocyanins 209 G674 Leaf; size Dev and morph MYB-(R1) Darkgreen leaves, 210 (20-120) R2R3 upwardly oriented; reduced size 211 G736Leaf; flowering time Dev and morph; Z-Dof Altered leaf shape; 212(54-111) flowering time later flowering 213 G903 Leaf Dev and morphZ-C2H2 Altered leaf 214 (68-92) morphology 215 G917 Leaf; seed oil Devand morph MADS Altered leaf development; 216 (2-57) and protein contentseed biochemistry altered seed oil and protein content 217 G921 Leaf Devand morph WRKY Serrated leaves 218 (146-203) 219 G922 Leaf; size Dev andmorph SCR Altered development, 220 (225-242) dark green color; reducedsize 221 G932 Leaf; size Dev and morph MYB-(R1)R2R3 Altered development,220 (225-242) dark green color; reduced size 223 G599 Leaf; size Dev andmorph DBP Altered leaf shape; 224 (187-219, small plant 264-300) 225G804 Leaf; size Dev and morph PCF Altered leaf shape, 226 (54-117) smallplant 227 G1062 Light response; Dev and morph HLH/MYC Constitutive 228(308-359) morphology; photomorphogenesis; other; seed slow growth;altered seed shape 229 G1322 Light response; size Dev and morphMYB-(R1)R2R3 Photomorphogenesis 230 (26-130) in the dark; reduced size231 G1331 Light response; Dev and morph; MYB-(R1) Constitutive 232(8-109) morphology; other; seed biochemistry R2R3 photomorphogenesis;seed oil and multiple developmental protein content alterations; alteredseed oil and protein content 233 G1521 Light response Dev and morphRING/C3HC4 Constitutive 234 (39-80) photomorphogenesis 235 G183 Lightresponse; Dev and morph; WRKY Constitutive 236 (307-363) seed proteincontent seed biochemistry photomorphogenesis; altered seed proteincontent 237 G2555 Light response Dev and morph HLH/MYC Constitutive 238(175-245) photomorphogenesis 239 G375 Light response Dev and morph Z-DofUpward pointing leaves 240 (75-103) 241 G1007 Morphology; other Dev andmorph AP2 Multiple 242 (TBD) developmental alterations 243 G1010Morphology; other Dev and morph ABI3/VP-1 Multiple 244 (33-122)developmental alterations 245 G1014 Morphology; other Dev and morphABI3/VP-1 Multiple 246 (90-172) trichome developmental defects; reducedtrichomes 247 G1035 Morphology; other Dev and morph bZIP Multiple 248(39-91) developmental alterations 249 G1046 Morphology; other Dev andmorph bZIP Multiple 250 (79-138) developmental alterations 251 G1049Morphology; Dev and morph; bZIP Multiple 252 (77-132) other; seed seedbiochemistry developmental protein content alterations; altered seedprotein content 253 G1069 Morphology: other Dev and morph; AT-hookMultiple 254 (67-74) seed oil content seed biochemistry developmentalalterations; altered seed oil content 255 G1070 Morphology: other Devand morph AT-hook Several developmental 256 (98-120) defects 257 G1076Morphology; other Dev and morph AT-hook Lethal when 258 (82-89)overexpressed 259 G1089 Morphology; other Dev and morph BZIPT2Developmental defects 260 (425-500) at seeding stage 261 G1093Morphology: other Dev and morph RING/C3H2C3 Multiple morphological 262(105-148) alterations 263 G1127 Morphology: other Dev and morph AT-hookMultiple developmental 264 (103-110, alterations 155-162) 265 G1131Morphology: other; Dev and morph; HLH/MYC Multiple developmental 266(173-220) seed protein content alterations; altered seed protein content267 G1145 Morphology; other; Dev and morph; bZIP Multiple developmental268 (227-270) seed oil and seed biochemistry alterations; reducedprotein content seed size, altered seed shape; altered seed oil andprotein content 269 G1229 Morphology: other; Dev and morph; HLH/MYCSeveral developmental 270 (102-160) seed oil and seed biochemistrydefects; altered seed protein content content oil and protein 271 G1246Morphology; other Dev and morph; MYB-(R1) Multiple developmental 272(27-139) seed protein seed biochemistry R2R3 alterations; alteredcontent seed protein content 273 G1255 Morphology; other Dev and morphZ-CO-like Reduced apical 274 (18-56) seed dominance; increased seed size275 G1304 Morphology: other Dev and morph MYB-(R1) Lethal when 276(13-118) R2R3 overexpressed 277 G1318 Morphology: other Dev and morphMYB-(R1) Multiple developmental 378 (20-123) R2R3 alterations 279 G1320Morphology: other Dev and morph MYB-(R1) Multiple developmental 280(5-108) R2R3 alterations 281 G1330 Morphology: other Dev and morphMYB-(R1) Multiple developmental 282 (28-134) R2R3 alterations 283 G1352Morphology: other Dev and morph Z-C2H2 Multiple developmental 284(108-129, alterations 167-188) 285 G1354 Morphology: other Dev and morphNAC Multiple developmental 286 (TBD) alterations 287 G1360 Morphology:other Dev and morph NAC Lethal when overexpressed 288 (18-174) 289 G1364Morphology: other Dev and morph CAAT Lethal when overexpressed 290(29-120) 291 G1379 Morphology: other Dev and morph AP2 Multipledevelopmental 292 (18-85) alterations 293 G1384 Morphology: other Devand morph AP2 Abnormal inflorescence 294 (TBD) and flower development295 G1399 Morphology: other Dev and morph AT-hook Multiple developmental296 (86-93) alterations 297 G1415 Morphology: other Dev and morph AP2Multiple developmental 298 (TBD) alterations 299 G1417 Morphology:other; Dev and morph; WRKY Reduced seeding 300 (239-296) seed oil seedbiochemistry germination and vigor; increases in 18:2, decrease in 18:3301 G1442 Morphology: other Dev and morph GRF-like Multipledevelopmental 302 (172-223) alterations 303 G1454 Morphology: other; Devand morph; NAC Multiple developmental 304 (9-178) seed oil and seedbiochemistry alteration; altered protein content seed oil and proteincontent 305 G1459 Morphology; other Dev and morph NAC Multipledevelopmental 306 (10-152) alterations 307 G1460 Morphology: other; Devand morph NAC Multiple developmental 308 (TBD) seed protein content seedbiochemistry alterations; altered seed protein content 309 G147Morphology: other Dev and morph MADS Multiple developmental 310 (2-57)defects 311 G1471 Morphology: other; Dev and morph; Z-C2H2 Multipledevelopmental 312 (49-70) seed oil seed biochemistry alterations;defects increased seed oil content 313 G1475 Morphology: other Dev andmorph Z-C2H2 Multiple developmental 314 (51-73) alterations 315 G1477Morphology: other Dev and morph Z-C2H2 Multiple developmental 316(29-48) alterations 317 G1487 Morphology: other; Dev and morph: GATA/ZnMultiple developmental 318 (251-276) seed oil and seed biochemistryalterations; altered protein content seed oil and protein content 319G1492 Morphology: other Dev and morph GARP Multiple developmental 320(34-83) alterations 321 G1531 Morphology: other; Dev and morph;RING/C3HC4 Multiple developmental 322 (41-77) seed; seed protein seedbiochemistry alterations; pale seed; content altered seed proteincontent 323 G1540 Morphology: other Dev and morph HB Reduced cell 324(35-98) differentiation in meristem 325 G1544 Morphology: other Dev andmorph HB Multiple developmental 326 (64-124) alterations 327 G156Morphology: other; Dev and morph MADS Multiple developmental 328 (2-57)seed defects; seed color alteration 329 G1584 Morphology: other Dev andmorph HB Multiple developmental 330 (TBD) alteration 331 G1587Morphology: other Dev and morph HB Multiple developmental 332 (61-121)alteration 333 G1588 Morphology: other Dev and morph HB Multipledevelopmental 334 (66-124) alteration 335 G1589 Morphology: other Devand morph HB Multiple developmental 336 (384-448) seed protein contentseed biochemistry alterations; altered seed protein content 337 G160Morphology: other Dev and morph MADS Multiple developmental 338 (7-62)defects 339 G1636 Morphology: other Dev and morph MYB- Pale green,smaller 340 (100-165) related plants 341 G1642 Morphology: other Dev andmorph MYB- Multiple developmental 342 (TBD) (R1)R2R3 alterations 343G1747 Morphology: other; Dev and morph; MYB-(R1) Multiple developmental344 (11-114) seed protein contcent seed biochemistry R2R3 alterations;altered seed protein content 345 G1749 Morphology: other Dev and morphAP2 Multiple developmental 346 (84-155) alterations; formation ofnecrotic lesions 347 G1751 Morphology: other Dev and morph AP2 Multipledevelopmental 348 (TBD) alterations 349 G1752 Morphology: other Dev andmorph AP2 Multiple developmental 350 (83-151) alterations 351 G1763Morphology: other Dev and morph AP2 Lethal when overexpressed 352(140-209) 353 G1766 Morphology: other Dev and morph NAC Multipledevelopmental 354 (10-153) alterations 355 G1767 Morphology: other Devand morph; SCR Multiple developmental 356 (255-272) seed oil contentseed biochemistry alterations; altered seed oil content 357 G1778Morphology: other Dev and morph GATA/Zn Lethal when overexpressed 358(94-119) 359 G1789 Morphology: other; Dev and morph; MYB-related Delayeddevelopment; 360 (1-50) seed protein content seed biochemistry alteredseed protein content 361 G1790 Morphology: other Dev and morphMYB(R1)R2R3 Lethal when overexpressed 362 (217-316) 363 G1791Morphology: other Dev and morph AP2 Multiple developmental 364 (TBD)alterations 365 G1793 Morphology: other; Dev and morph; AP2 Multipledevelopmental 366 (179-255, seed oil seed biochemistry alterations;increased 281-349) seed oil content 367 G1795 Morphology: other; Dev andmorph AP2 Multiple developmental 368 (12-80) triichome alterations;reduced trichomes 369 G1800 Morphology: other Dev and morph AP2 Multipledevelopmental 370 (TBD) alterations 371 G1806 Morphology: other Dev andmorph bZIP Multiple developmental 372 (165-225) alterations 373 G1811Morphology: other Dev and morph ABI3/VP-1 Multiple developmental 374(TBD) alterations 375 G182 Morphology: other Dev and morph WRKY Multipledevelopmental 376 (217-276) alterations 377 G1835 Morphology: other Devand morph GATA/Zn Small, spindly plant 378 (224-296) 379 G1836Morphology: other Dev and morph CAAT Pale green 380 (30-164) 381 G1838Morphology: other; Dev and morph; AP2 Multiple developmental 382(229-305, seed oil content seed biochemistry alterations; increaed330-400) seed oil content 383 G1843 Morphology: other Dev and morph MADSMultiple developmental 384 (2-57) alterations 385 G1853 Morphology:other Dev and morph AKR Lethal when overexpressed 386 (entire protein)387 G1855 Morphology: other Dev and morph AKR Slow growth 388 (entireprotein) 389 G187 Morphology: other Dev and morph WRKY Variety of 390(172-228) morphological alterations 391 G1881 Morphology: other Dev andmorph Z-CO-like Multiple developmental 392 (5-28, alterations 56-79) 393G1882 Morphology: other Dev and morph Z-Dof Lethal when overexpressed394 (97-125) 395 G1883 Morphology: other Dev and morph Z-Dof Multipledevelopmental 396 (82-124) alterations 397 G1884 Morphology: other Devand morph Z-Dof Multiple developmental 398 (43-71) alterations 399 G1891Morphology: other Dev and morph Z-Dof Multiple developmental 400 (27-69)alterations 401 G1896 Morphology: other Dev and morph Z-Dof Multipledevelopmental 402 (43-85) alterations 403 G1898 Morphology: other Devand morph Z-Dof Lethal when overexpressed 404 (31-59) 405 G1902Morphology: other; Dev and morph; Z-Dof Multiple developmental 406(31-59) seed oil content seed biochemistry alterations; increased seedoil content 407 G1904 Morphology: other Dev and morph Z-Dof Multipledevelopmental 408 (53-95) alterations 409 G1906 Morphology: other Devand morph Z-Dof Multiple developmental 410 (19-47) alterations 411 G1913Morphology: other Dev and morph Z-Dof Lethal when overexpressed 412(27-55) 413 G1914 Morphology: other Dev and morph Z-C2H2 Multipledevelopmental 414 (195-216, alterations 245-266) 415 G1925 Morphology:other Dev and morph NAC Multiple developmental 416 (6-150) alterations417 G1929 Morphology: other Dev and morph Z-CO-like Slow growth, delayed418 (31-53) development 419 G1930 Morphology: other Dev and morph AP2Multiple developmental 420 (59-124) alterations 421 G195 Morphology:other Dev and morph WRKY Multiple developmental 422 (183-239) defects423 G1954 Morphology: other Dev and morph HLH/MYC Lethal whenoverexpressed 424 (187-259) 425 G1958 Morphology: other; Dev and morph;GARP Reduced size and root 426 (230-278) seed protein content seedbiochemistry mass in plates; altered seed protein content 427 G196Morphology: other; Dev and morph; WRKY Multiple developmental 428(223-283) seed protein content seed biochemistry alterations; alteredseed protein content 429 G1965 Morphology: other Dev and morph Z-DofLethal when overexpressed 430 (27-55) 431 G1976 Morphology: other Devand morph Z-C2H2 Multiple developmental 432 (219-323) alterations 433G2057 Morphology: other Dev and morph TEO Multiple developmental 434(TBD) alterations 435 G2107 Morphology: other Dev and morph AP2 Multipledevelopmental 436 (TBD) alterations 437 G211 Morphology: other Dev andmorph MYB-(R1) Multiple developmental 438 (24-137) R2R3 alterations 439G2133 Morphology: other; Dev and morph; AP2 Multiple developmental 440(11-83) flowering time; flowering time alterations; late seed proteinflowering; altered seed content protein content 441 G2134 Morphology:other Dev and morph AP2 Multiple developmental 442 (TBD) alterations 443G2151 Morphology: other; Dev and morph; AT-hook Multiple developmental444 (93-113, seed oil and seed biochemistry alterations; altered124-144) protein content seed oil and protein content 445 G2154Morphology: other Dev and morph AT-hook Multiple developmental 446(97-119) alterations 447 G2157 Morphology: other Dev and morph AT-hookMultiple developmental 448 (82-120, alteration 164-107) 449 G2181Morphology: other Dev and morph NAC Multiple developmental 450 (22-169)alterations 451 G221 Morphology: other Dev and morph MYB-(R1) Multipledevelopmental 452 (21-125) R2R3 alteration 453 G2290 Morphology: otherDev and morph WRKY Multiple developmental 454 (147-205) alterations 455G2299 Morphology: other Dev and morph AP2 Multiple developmental 456(48-115) alterations 457 G2340 Morphology: other; Dev and morph;MYB-(R1) Tissue necrosis; multiple 458 (14-120) seed oil and seedbiochemistry R2R3 developmental alterations; protein content alteredseed oil and protein content 459 G2346 Morphology: other Dev and morphSBP Enlarged seedlings 460 (59-135) 461 G237 Morphology; other Dev andmorph MYB-(R1) Multiple developmental 462 (11-113) R2R3 alterations 463G2373 Morphology: other; Dev and morph; TH Multiple developmental 464(290-350) seed protein content seed biochemistry alterations; alteredseed protein content 465 G2276 Morphology: other; Dev and morph; THSeeding lethality; 466 (79-178, seed oil seed biochemistry altered seedprotein 336-408) protein content 467 G24 Morphology: other Dev and morphAP2 Reduced size and 468 (25-93) necrotic patches 469 G2424 Morphology:other Dev and morph MYB-(R1) Multiple developmental 470 (107-219) R2R3alterations 471 G2505 Morphology: other Dev and morph NAC Lethal whenoverexpressed 472 (10-159) 473 G2512 Morphology: other Dev and morph AP2Multiple developmental 474 (79-139) alterations 475 G2513 Morphology:other Dev and morph AP2 Multiple developmental 476 (TBD) alterations 477G2519 Morphology: other Dev and morph HLH/MYC Multiple developmental 478(1-65) alterations 479 G2520 Morphology: other; Dev and morph; HLH/MYCMultiple developmental 480 (135-206) seed oil and seed biochemistryalterations; altered protein content seed oil and protein content 481G2533 Morphology: other; Dev and morph; NAC Multiple developmental 482(11-186) seed protein content seed biochemistry alterations; alteredseed protein content 483 G2534 Morphology: other Dev and morph NACLethal when overexpressed 484 (10-157) 485 G2573 Morphology: other; Devand morph; AP2 Multiple developmental 486 (31-98) seed oil and seedbiochemistry alterations; altered protein content seed oil and proteincontent 487 G2589 Morphology: other Dev and morph MADS Multipledevelopmental 488 (2-57) alterations 489 G2687 Morphology: other Dev andmorph AP2 Multiple developmental 490 (51-120) alterations 491 G27Morphology: other Dev and morph AP2 Abnormal development, 492 (37-104)small 493 G2720 Morphology: other; Dev and morph; MYB-(R1) Multipledevelopment 494 (10-114) seed oil and seed biochemistry R2R3 alteration;altered protein content seed oil and protein content 495 G2787Morphology: other; Dev and morph; AT-hook Multiple developmental 496(172-192, seed oil content seed biochemistry alterations; altered226-247, seed oil content 256-276, 290-311, 245-366) 497 G2789Morphology: other Dev and morph AT-hook Multiple developmental 498(53-73, alterations 121-165) 449 G31 Morphology: other Dev and morph AP2Multiple developmental 500 (TBD) alterations 501 G33 Morphology: otherDev and morph AP2 Multiple developmental 502 (50-117) defects 503 G342Morphology: other; Dev and morph; GATA/Zn Multiple developmental 504(155-190) seed oil and seed biochemistry alterations; altered proteincontent seed oil and protein content 505 G352 Morphology: other Dev andmorph Z-C2H2 Multiple developmental 506 (99-119, alterations 166-186)507 G357 Morphology: other Dev and morph Z-C2H2 Developmental defect 508(7-29) 509 G358 Morphology: other Dev and morph Z-C2H2 Lethal whenoverexpressed 510 (124-135, 188-210) 511 G360 Morphology: other Dev andmorph Z-C2H2 Multiple development 512 (42-62) alterations 513 G362 Size;Morphology: Dev and morph; Z-C2H2 Reduced size; increased 514 (62-82)other; trichome; flowering time; pigmentation in seed flowering time;seed biochemistry embryos and other seed protein organs; ectopic contenttrichome formation; increased trichome number; late flowering; alteredprotein content 515 G364 Morphology: other Dev and morph Z-C2H2Developmental defect 516 (54-76) 517 G365 Morphology: other Dev andmorph Z-C2H2 Multiple developmental 518 (70-90) alterations 519 G367Morphology: other Dev and morph Z-C2H2 Lethal when overexpressed 520(63-84) 521 G373 Morphology: other Dev and morph RING/ Multipledevelopmental 522 (129-168) C3HC4 alterations 523 G396 Morphology:other; Dev and morph HB Altered leaf coloration 524 (159-220) size andshape reduced fertility; small plant 525 G431 Morphology: other Dev andmorph HB Developmental defect, 526 (286-335) sterile 527 G479Morphology: other Dev and morph SBP Multiple developmental 528 (70-149)alterations 529 G546 Morphology: other Dev and morph RING/C3H2C3 Slowgrowth and 530 (114-155) development; increased anthocyanin pigmentation531 G551 Morphology: other Dev and morph HB Multiple developmental 532(73-133) alterations 533 G578 Morphology: other Dev and morph bZIPLethal when overexpressed 534 (36-96) 535 G596 Morphology: other Dev andmorph AT-hook Multiple developmental 536 (89-96) alterations 537 G617Morphology: other Dev and morph TEO Multiple developmental 538 (64-118)alterations 539 G620 Morphology: other; Dev and morph; CAAT Multipledevelopmental 540 (20-118) seed protein content seed biochemistryalterations; altered seed protein content 541 G625 Morphology: other Devand morph AP2 Lethal when 542 (52-119) overexpressed 543 G658Morphology: other Dev and morph MYB-(R1) Developmental defect 544(2-105) R2R3 545 G716 Morphology: other Dev and morph ARF Multipledevelopmental defects 546 (24-355) 547 G725 Morphology: other Dev andmorph GARP Developmental defect 548 (39-87) 549 G727 Morphology: otherDev and morph GARP Multiple morphological 550 (226-269) alterations 551G740 Morphology: other Dev and morph Z-CLDSH Slow growth 552 (24-42,232-268) 553 G770 Morphology: other Dev and morph NAC Multipledevelopmental 554 (19-162) alterations 555 G858 Morphology: other Devand morph MADS Multiple developmental 556 (2-57) alterations 557 G865Morphology: other; Dev and morph; AP2 Altered morphology 558 (36-103)seed protein content seed biochemistry increased see protein 559 G872Morphology: other Dev and morph AP2 Multiple developmental 560 (18-85)alterations 561 G904 Morphology: other Dev and morph RING/C3H2C3Multiple developmental 562 (117-158) alterations 563 G910 Morphology:other; Dev and morph; Z-CO-like Multiple developmental 564 (14-37,flowering time flowering time alterations; late 77-103) flowering 565G912 Morphology: other; Dev and morph; AP2 Dark green color; 566(51-118) size; sugar sugar sensing; small plant; reduced sensing;flowering cotyledon expansion flowering time in glucose; late timeflowering 567 G290 Morphology: other Dev and morph WRKY Multipledevelopmental 568 (152-211) alterations 569 G939 Morphology: other; Devand morph EIL Pale seedlings on agar; 570 (97-106) size reduced size 571G963 Morphology: other; Dev and morph; NAC Slowed growth rate; 572 (TBD)seed protein seed biochemistry altered seed protein content content 573G979 Morphology: other; Dev and morph AP2 Several development 574(63-139, seed defects; altered seed 165-233) development, ripening andgermination 575 G987 Morphology: other Dev and morph SCR Developmentaldefects 576 (428-432, 704-708) 577 G993 Morphology: other Dev and morph;AP2 Multiple developmental 578 (69-134) seed protein content seedbiochemistry alterations; altered seed protein content 579 G681Morphology: other; Dev and morph; MYB-(R1) Multiple developmental 580(14-120) leaf glucosinolates leaf biochemistry R2R3 alterations;overexpression results in an increased in M39480 581 G1482 Root Dev andmorph Z-CO-like Increased root growth 582 (5-63) 583 G225 Root; trichomeDev and morph MYB-related Increased root hairs; 584 (39-76) glabrous,lack of trichomes 585 G226 Root; trichome; Dev and morph; MYB-relatedIncreased root hair; 586 (28-78) seed protein content seed biochemistryglabrous, lack of trichomes; increased seed protein 587 G9 Root Dev andmorph AP2 Increased root mass 588 (62-127) 589 G1040 Seed Dev and morphGARP Smaller and more 590 (109-158) rounded seeds 591 G2114 Seed Dev andmorph AP2 Increased seed size 592 (221-297, 323-393) 593 G450 Seed;size; Dev and morph; IAA Increased seed size; 594 (TBD) seed proteinseed biochemistry reduced plant size; content altered seed proteincontent 595 G584 Seed Dev and morph HLH/MYC Large seeds 596 (401-494)597 G668 Seed Dev and morph MYB-(R1) Reduced seed color 598 (13-113)R2R3 599 G1050 Senescence Dev and morph bZIP Delayed senescence 600(372-425) 601 G1463 Senescence Dev and morph NAC Premature senescence602 (9-156) 603 G1944 Senescence; size; Dev and morph; AT-hook Earlysenescence; 604 (87-100) seed protein content seed biochemistry reducedsize; altered seed protein content 605 G2383 Senescence; seed Dev andmorph; TEO Early senescence; 606 (89-149) protein content seedbiochemistry altered seed protein content 607 G571 Senescence; Dev andmorph; bZIP Delayed senescence; 608 (160-220) flowering time floweringtime late flowering 609 G636 Senescence; size Dev and morph TH Prematuresenescence; 610 (55-145, reduced size 405-498) 611 G878 Senescence; Devand morph; WRKY Delayed senescence; 612 (250-305, flowering timeflowering time late flowering 415-475) 613 G1134 Silique Dev and morphHLH/MYC Siliques with altered 614 (198-247) shape 615 G1008 Size Dev andmorph AP2 Small plant 616 (96-163) 617 G1020 Size Dev and morph AP2 Verysmall T1 plants 618 (28-95) 619 G1023 Size Dev and morph AP2 Reducedsize 620 (128-195) 621 G1053 Size Dev and morph bZIP Small plant 622(74-120) 623 G1137 Size Dev and morph HLH/MYC Small T1 plants 624(264-314) 625 G1181 Size Dev and morph HS Small T1 plants 626 (24-114)627 G1228 Size Dev and morph HLH/MYC Reduced size 628 (179-233) 629G1277 Size Dev and morph AP2 Small plant 630 (18-85) 631 G1309 Size Devand morph MYB-(R1) Small plant 632 (9-114) R2R3 633 G1314 Size; sugarDev and morph; MYB-(R1) Reduced size; reduced 634 (14-116) sensing; seedsugar sensing; R2R3 seedling vigor on high protein content seedbiochemistry glucose; altered seed protein content 635 G1317 Size Devand morph MYB-(R1) Reduced size 636 (13-118) R2R3 637 G1323 Size; seedoil Dev and morph; MYB-(R1) Small T1 plants, dark 638 (15-116) andprotein content seed biochemistry R2R3 green; decreased seed oil,increased seed protein 639 G1332 Size; trichome; seed Dev and morph;MYB-(R1) Reduced size; reduced 640 (13-116) oil and protein seedbiochemistry R2R3 trichome densitry; content altered seed oil andprotein content 641 G1334 Size Dev and morph CAAT Small, dark green 642(18-190) 643 G1381 Size Dev and morph AP2 Reduced size 644 (68-135) 645G1382 Size Dev and morph WRKY Small plant 646 (210-266. 385-437) 647G1435 Size; flowering Dev and morph; GARP Increased plant size; 648(146-194) time flowering time late flowering 649 G1537 Size Dev andmorph HB Small T1 plants with 650 (14-74) altered development 651 G1545Size Dev and morph HB Reduced size 652 (54-117) 653 G1641 Size; seed oilDev and morph; MYB- related Small plant; altered 654 (139-200) andprotein content seed biochemistry seed oil and protein content 655 G165Size; seed Dev and morph; MADS Reduced size; altered 656 (7-62) contentseed biochemistry seed protein content 657 G1652 Size; seed oil Dev andmorph; HLH/MYC Reduced size; altered 658 (143-215) and protein contentseed biochemistry seed oil and protein content 659 G1655 Size Dev andmorph HLH/MYC Small plant 660 (134-192) 661 G1671 Size Dev and morph NACReduced size 662 (TBD) 663 G1756 Size; seed Dev and morph WRKY Reducedsize; altered 664 (TBD) protein content seed biochemistry seed proteincontent 665 G1757 Size; seed Dev and morph; WRKY Small plant; altered666 (158-218) protein content seed biochemistry seed protein content 667G1782 Size Dev and morph CAAT Small, spindly plant 668 (166-238) 669G184 Size Dev and morph WRKY Small plant 670 (295-352) 671 G1845 SizeDev and morph AP2 Small plant 672 (140-207) 673 G1879 Size; seed oil Devand morph; HLH/MYC Reduced size; altered 674 (107-176) and proteincontent seed biochemistry seed oil and protein content 675 G1888 SizeDev and morph Z-CO-like Reduced size, dark 676 (5-50) green leaves 677G189 Size; seed protein Dev and morph; WRKY Increased leaf size; 678(240-297) content seed biochemistry altered seed protein content 679G1939 Size Dev and morph PCF Reduced size 680 (40-102) 681 G194 Size Devand morph WRKY Small plant 682 (174-230) 683 G1973 Size Dev and morphHLH/MYC Reduced size 684 (335-406) 685 G21 Size; seed oil Dev and morph;AP2 Reduced size; altered 686 (97-164) and protein content seedbiochemistry seed oil and protein content 687 G2132 Size; seed oil Devand morph; AP2 Reduced size; altered 688 (TBD) and protein content seedbiochemistry seed oil and protein content 689 G2145 Size Dev and morphHLJH/MYC Reduced size 690 (166-243) 691 G23 Size Dev and morph AP2 SmallT1 plants 692 (61-117) 693 G2313 Size Dev and morph MYB-related Reducedsize 694 (TBD) 695 G2344 Size Dev and morph CAAT Reduced size, slowgrowth 696 (TBD) 697 G2430 Size Dev and morph GARP Increased leaf size,698 (425-478) faster development 699 G2517 Size Dev and morph WRKYReduced size 700 (118-234) 701 G2521 Size Dev and morph HLH/MYC Reducedsize 702 (145-213) 703 G258 Size; seed oil Dev and morph; MYB-(R1)Reduced size; altered 704 (24-124) and protein content seed biochemistryR2R3 seed oil and protein content 705 G280 Size; seed Dev and morph;AT-hook Reduced size; altered 706 (97-104, protein content seedbiochemistry seed protein content 130-137- 155-162, 185-192) 707 G3 SizeDev and morph AP2 Small plant 708 (28-95) 709 G343 Size Dev and morphGATA/Zn Small plant 710 (178-214) 711 G363 Size Dev and morph Z-C2H2Small plant 712 (87-108) 713 G370 Size Dev and morph Z-C2H2 Reducedsize, shiny 714 (97-117) leaves 715 G385 Size Dev and morph HB Smallplant, short 716 (60-123) inflorescence stems, dark green 717 G439 SizeDev and morph AP2 Small plant 718 (110-177) 719 G440 Size Dev and morphAP2 Small plant 720 (122-189) 721 G5 Size Dev and morph AP2 Small plant722 (149-216) 723 G550 Size Dev and morph Z-Dof Small plant 724(134-180) 725 G670 Size Dev and morph MYB-(R1) Small plant 726 (14-122)R2R3 727 G760 Size Dev and morph NAC Reduced size 728 (12-156) 729 G831Size Dev and morph AKR Reduced size 730 (470-591) 731 G864 Size Dev andmorph AP2 Small plant 732 (119-186) 733 G884 Size Dev and morph WRKYReduced size 734 (227-285, 407-465) 735 G898 Size; seed oil Dev andmorph; RING/C3HC4 Reduced size; altered 736 (148-185) and proteincontent seed biochemistry seed oil and protein content 737 G900 Size Devand morph Z-CO-like Reduced size 738 (6-28, 48-74) 739 G913 Size;flowering Dev and morph; AP2 Small plant; late 740 (62-128) timeflowering time flowering 741 G937 Size Dev and morph GARP Slightlyreduced size 742 (197-246) 743 G960 Size Dev and morph NAC Small plant744 (13-156) 745 G991 Size; seed oil Dev and morph; IAA Slightly reducedsize; 746 (7-14,48- and protein content seed biochemistry altered seedoil and 59,82-115, protein content 128-164) 747 G748 Stem; flowering Devand morph; Z-Dof More vascular bundles 748 (112-140) time flowering timein stem; late flowering 749 G247 Trichome; seed Dev and morph; MYB-(R1)Altered trichome 750 (15-116) seed protein seed biochemistry R2R3distribution; altered content seed protein content 751 G585 Trichome Devand morph HLH/MYC Reduced trichome denisty 752 (436-501) 753 G634Trichome; seed Dev and morph; TH Increased trichome 754 (62-147, proteincontent seed biochemistry density and size; 189-245) altered seedprotein content 755 G676 Trichome Dev and morph MYB-(R1) reducedtrichomes 756 (17-119) R2R3 757 G682 Trichome Dev and morph MYB-relatedGlabrous, lack of 758 (27-63) trichomes 759 G635 Variegation Dev andmorph TH 760 (239-323) 761 G1068 Sugar sensing Sugar sensing AT-hookReduced cotyledon 762 (143-150) expansion in glucose 763 G1225 Sugarsensing; seed Sugar sensing; HLH/MYC Better germination on 764 (78-147)oil and protein biochemistry sucrose and glucose content media; alteredseed oil and protein content 765 G1337 Sugar sensing Sugar sensingZ-CO-like Decreased germination 766 (9-75) on sucrose medium 767 G1759Sugar sensing Sugar sensing MADS Reduced germination 768 (2-57) on highglucose 769 G1804 Sugar sensing; Sugar sensing; bZIP Altered sugarsensing; 770 (357-407) flowering time flowering time late flowering 771G207 Sugar sensing Sugar sensing MYB-(R1) Decreased germination 772(6-106) R2R3 on glucose medium 773 G218 Sugar sensing; Sugar sensing;MYB-(R1) Reduced cotyledon 774 (TBD) seed oil content seed biochemistryR2R3 expansion in glucose; altered seed oil content 775 G241 Sugarsensing; seed Sugar sensing; MYB-(R1) Decreased germination 776 (14-114)oil and protein seed biochemistry R2R3 and growth on glucose contentmedium; decreased seed oil, altered protein content 777 G254 Sugarsensing Sugar sensing MYB-related Decreased germination 778 (62-106) andgrowth on glucose medium 779 G26 Sugar sensing Sugar sensing AP2Decreased germination 780 (67-134) and growth on glucose medium 781 G263Sugar sensing Sugar sensing HS Decreased root growth 728 (TBD) onsucrose medium, root specific expression 783 G308 Sugar sensing Sugarsensing SCR No germination on 784 (270-247) glucose medium 785 G38 Sugarsensing Sugar sensing AP2 Reduced germination on 786 (76-143) glucosemedium 787 G43 Sugar sensing Sugar sensing AP2 Decreased germination 788(104-172) and growth on glucose medium 789 G536 Sugar sensing Sugarsensing GF14 Decreased germination 790 (226-233) and growth on glucosemedium 791 G567 Sugar sensing; seed Sugar sensing; seed b-ZIP Decreasedseedling 792 (210-270) oil and biochemistry vigor on high glucose;protein content altered seed oil and protein content 793 G680 Sugarsensing; Sugar sensing; MYB-related Reduced germination 794 (24-70)flowering time flowering time on glucose medium; late flowering 795 G867Sugar sensing Sugar sensing AP2 Better seedling vigor 796 (59-124) onsucrose medium 797 G956 Sugar sensing Sugar sensing NAC Reducedgermination 798 (TBD) on glucose medium 799 G996 Sugar sensing Sugarsensing MYB-(R1) Reduced germination 800 (14-114) R2R3 on glucose medium801 G1946 Seed glucosinolates Seed biochemistry HS Increased in M3950;802 (32-130) oil protein increased oil content; content decreasedprotein content 803 G217 Seed oil composition Seed biochemistryMYB-related Increased in 20:2 804 (8-67) 805 G2192 Seed oil compositionSeed biochemistry bZIP-NIN Altered composition 806 (600-700) 807 G504Seed oil Seed biochemistry NAC Altered seed oil 808 (TBD) composition;seed composition and content; protein content altered seed proteincontent 809 G622 Seed oil composition Seed biochemistry ABI3/VP-1Decreased 18:2 fatty acid 810 (TBD) 811 G778 Seed oil composition Seedbiochemistry HLH/MYC Increased seed 18:1 fatty acid 812 (220-267) 813G791 Seed oil composition Seed biochemistry HLH/MYC Altered seed fattyacid 814 (75-143) composition 815 G861 Seed oil composition; Seedbiochemistry MADS Increase in 16:1; 816 (2-57) seed oil content alteredseed oil content 817 G938 Seed oil composition Seed biochemistry EILAltered seed fatty acid 818 (96-104) composition 819 G965 Seed oilcomposition Seed biochemistry HB Increased in 18:1 820 (423-486) 821G1143 Seed oil and Seed biochemistry HLH/MYC Altered seed oil and 822(33-82) protein content protein content 823 G1190 Seed oil content Seedbiochemistry AKR Increased content 824 (entire protein) 825 G1198 Seedoil and Seed biochemistry bZIP Altered seed oil and 826 (173-223)protein content protein content 827 G1226 Seed oil and protein Seedbiochemistry HLH/MYC Altered seed oil and 828 (115-174) content proteincontent 829 G1451 Seed oil content Seed biochemistry ARF Altered seedoil content 830 (22-357) 831 G1478 Seed oil and Seed biochemistry;Z-CO-like Altered seed oil, 832 (32-76) protein content; flowering timeprotein content; late flowering time flowering 833 G1496 Seed oilcontent Seed biochemistry HLH/MYC Altered seed oil 834 (184-248) content835 G1526 Seed oil content Seed biochemistry SWI/SNF Increased seed oil836 (493-620, content 864-1006) 837 G1543 Seed oil content Seedbiochemistry HB Decreased seed oil 838 (135-195) 839 G162 Seed oil andSeed biochemistry MADS Altered seed oil 840 (2-57) protein contentcontent; altered seed oil and protein content 841 G1640 Seed oil contentSeed biochemistry MYB-(R1) Increased seed oil 842 (14-115) R2R3 843G1644 Seed oil and Seed biochemistry MYB-(R1) Altered seed oil, 844(39-102) protein content R2R3 protein content 845 G1646 Seed oil contentSeed biochemistry CAAT Altered seed oil content 846 (72-162) 847 G1672Seed oil content Seed biochemistry NAC Altered seed oil content 848(41-194) 849 G1677 Seed oil and Seed biochemistry NAC Altered seed oil,850 (17-181) protein content protein content 851 G1765 Seed oil and Seedbiochemistry NAC Altered seed oil and 852 (20-140) protein contentprotein content 853 G1777 Seed oil and Seed biochemistry RING/C3HC4Increased oil, 854 (124-247) protein content decreased protein content855 G1793 Seed oil content Seed biochemistry AP2 Increased seed oil 856(179-255, content 281-349) 857 G180 Seed oil content Seed biochemistryWRKY Decreased seed oil 858 (118-174) content 859 G192 Seed oil and Seedbiochemistry; WRKY Altered seed oil and 860 (128-185) protein content;flowering time protein content; late flowering time flowering 861 G1948Seed oil and Seed biochemistry AKR Altered seed oil and 862 (entireprotein) protein content protein content 863 G2123 Seed oil and Seedbiochemistry GF14 Altered seed oil and 864 (99-109) protein contentprotein content 865 G2138 Seed oil content Seed biochemistry AP2Increased seed oil 866 (TBD) content 867 G2139 Seed oil content Seedbiochemistry MADS Increased seed content 868 (14-69) 869 G2343 Seed oilcontent Seed biochemistry MYB-(R1) Altered seed oil content 870 (14-116)R2R3 871 G265 Seed oil and Seed biochemistry HS Altered seed oil 872(11-105) protein content and protein content 873 G2792 Seed oil contentSeed biochemistry HLH/MYC Increased seed oil content 874 (190-258) 875G2830 Seed oil and Seed biochemistry Z-C2H2 Altered seed oil and 876(245-266) protein content protein content 877 G286 Seed oil and Seedbiochemistry ENBP Altered seed oil and 878 (TBD) protein content proteincontent 879 G291 Seed oil content Seed biochemistry MISC Increased seedoil content 880 (132-160) 881 G427 Seed oil and Seed biochemistry HBIncreased oil content; 882 (307-370) protein content decreased proteincontent 883 G509 Seed oil and protein Seed biochemistry NAC Altered seedoil and 884 (13-169) content protein content 885 G519 Seed oil andprotein Seed biochemistry NAC Altered seed oil and 886 (11-104) contentprotein content 887 G561 Seed oil content Seed biochemistry bZIP Alteredseed oil content 888 (248-308) 889 G590 Seed oil and Seed biochemistryHLH/MYC Altered seed oil and 890 (202-254) protein content proteincontent 891 G818 Seed oil content Seed biochemistry HS Increased content892 (70-162) 893 G849 Seed oil and Seed biochemistry BPF-1 Increasedseed oil, 894 (324-413. protein content altered protein content 504-583)895 G892 Seed oil and Seed biochemistry RING/C3H2C3 Altered seed oil,896 (177-270) protein content protein content 897 G961 Seed oil contentSeed biochemistry NAC Altered seed oil, 896 (15-140) content 899 G1465Seed oil and protein Seed biochemistry NAC Altered seed oil and 900(242-306) content protein content 901 G425 Seed oil content Seedbiochemistry HB Altered seed oil 902 (TBD) content 903 G347 Seed oil andSeed biochemistry Z-LSDlike Altered seed oil 904 (9-39,50- proteincontent protein content 70,80-127) 905 G1512 Seed oil and Seedbiochemistry RING/C3HC4 Altered seed oil and 906 (39-93) protein contentprotein content 907 G2069 Seed oil and Seed biochemistry bZIP Alteredseed oil and 908 (TBD) protein content protein content 909 G1852 Seedoil content Seed biochemistry AKR Altered seed oil content 910 (1-601)911 G1793 Seed oil content Seed biochemistry AP2 Altered seed oilcontent 912 (179-255, 281-349) 913 G761 Seed oil and Seed biochemistryNAC Altered seed oil and 914 (10-156) protein content protein content915 G1056 Seed oil content Seed biochemistry bZIP Altered seed oilcontent 916 (183-246) 917 G1447 Seed oil content Seed biochemistry MISCAltered seed oil content 918 (3-54, 124-156) 919 G323 Seed oil and Seedbiochemistry RING/C3HC4 Altered seed oil and 920 (48-96) protein contentprotein content 921 G176 Seed oil content Seed biochemistry WRKY Alteredseed oil content 922 (117-173, 234-290) 923 G174 Seed oil and proteinSeed biochemistry WRKY Altered seed oil and 924 (111-166, contentprotein content 283-339) 925 G715 Seed oil content Seed biochemistryCAAT Altered seed oil content 926 (60-132) 927 G588 Seed oil and proteinSeed biochemistry HLH/MYC Altered seed oil and 928 (309-376) contentprotein content 929 G1758 Seed oil and Seed biochemistry WRKY Alteredseed oil and 930 (109-165) protein content protein content 931 G2148Seed oil content Seed biochemistry HLH/MYC Altered seed oil 932(130-268) content 933 G2379 Seed oil content Seed biochemistry THAltered seed oil 934 (19-110, content 173-232) 935 G1462 Seed oilcontent Seed biochemistry NAC Altered seed oil content 936 (TBD) 937G1211 Seed oil and Seed biochemistry MISC Altered seed oil and 938(123-179) protein content protein content 939 G1048 Seed oil contentSeed biochemistry bZIP Altered seed oil content 940 (138-190) 941 G986Seed oil content Seed biochemistry WRKY Altered seed oil content 942(146-203) 943 G789 Seed oil content Seed biochemistry HLH/MYC Alteredseed oil content 944 (253-313) 945 G2085 Seed oil and Seed biochemistryRING/C3HC4 Altered seed oil and 946 (TBD) protein content proteincontent 947 G1783 Seed oil and protein Seed biochemistry MYB-relatedAltered seed oil and 948 (81 . . . 129) content protein content 949G2072 Seed oil and Seed biochemistry bZIP Altered seed oil and 950(90-149) protein content protein content 951 G931 Seed oil and proteinSeed biochemistry CAAT Altered seed oil and 952 (TBD) content proteincontent 953 G278 Seed oil and Seed biochemistry AKR Altered seed oil and954 (2-593) protein content protein content 955 G2421 Seed oil contentSeed biochemistry MYB-(R1) Altered seed oil content 956 (9-110) R2R3 957G2032 Seed oil content Seed biochemistry AKR Altered seed oil content958 (entire protein) 959 G1396 Seed oil and protein Seed biochemistryS1FA Altered seed oil and 960 (TBD) content protein content 961 G619Seed oil and Seed biochemistry ARF Altered seed oil and 962 (64-406)protein content protein content 963 G2295 Seed oil content Seedbiochemistry MADS Altered seed oil content 964 (2-57) 965 G312 Seed oilcontent Seed biochemistry SCR Altered seed oil 966 (320-336) content 967G1444 Seed oil and Seed biochemistry GRF-like Altered seed oil and 968(168-193) protein content protein content 969 G801 Seed oil content Seedbiochemistry PCF Altered seed oil content 970 (32-93) 971 G1950 Seed oilcontent Seed biochemistry AKR Altered seed oil content 972 (65-228) 973G958 Seed oil and protein Seed biochemistry NAC Altered seed oil and 974(7-156) content protein content 975 G1037 Seed oil and protein Seedbiochemistry GARP Altered seed oil and 976 (11-134, content proteincontent 200-248) 977 G2065 Seed oil content Seed biochemistry MADSAltered seed oil content 978 (TBD) 979 G2137 Seed oil and protein Seedbiochemistry WRKY Altered seed oil and 980 (109-168) content proteincontent 981 G746 Seed oil content Seed biochemistry RING/C3HC4 Alteredseed oil content 982 (139-178) 983 G2701 Seed oil and Seed biochemistryMYB-related Altered seed oil and 984 (33-81, protein content proteincontent 129-183) 985 G1819 Seed oil content Seed biochemistry CAATAltered seed oil content 986 (46-188) 987 G1227 Seed oil and proteinSeed biochemistry HLH/MYC Altered seed oil and 988 (183-244) contentprotein content 989 G2417 Seed oil content Seed biochemistry GARPAltered seed oil content 990 (235-285) 991 G2116 Seed oil content Seedbiochemistry bZIP Altered seed oil content 992 (150-210) 993 G647 Seedoil content Seed biochemistry Z-C3H Altered seed oil content 994(77-192) 995 G974 Seed oil and protein Seed biochemistry AP2 Alteredseed oil and 996 (81-140) content protein content 997 G1419 Seed proteincontent Seed biochemistry AP2 Increased seed protein 998 (69-137) 999G1634 Seed protein content Seed biochemistry MYC-related Altered seedprotein 1000 (129-180) content 1001 G1637 Seed protein content Seedbiochemistry MYB-related Altered seed protein 1002 (109-173) content1003 G1818 Seed protein content; Seed biochemistry; CAAT Increasedprotein 1004 (36-113) flowering time flowering time content; lateflowering 1005 G1820 Seed oil and protein Seed biochemistry CAAT Alteredseed oil, 1006 (70-133) content protein content 1007 G1903 Seed oil andprotein Seed biochemistry Z-Dof Altered seed oil and 1008 (134-180)content protein content 1009 G371 Seed oil and protein Seed biochemistryRING/C3HC4 Altered seed oil and 1010 (21-74) content protein content1011 G597 Seed protein content Seed biochemistry AT-hook Altered seedprotein content 1012 (97-104, 137-144) 1013 G1009 Seed protein contentSeed biochemistry AP2 Altered seed protein content 1014 (201-277,303-371) 1015 G170 Seed protein content Seed biochemistry MADS Alteredseed protein content 1016 (2-57) 1017 G1768 Seed protein content Seedbiochemistry SCR Altered seed protein content 1018 (54-413) 1019 G185Seed protein content Seed biochemistry WRKY Altered seed protein content1020 (113-172) 1021 G1931 Seed protein content Seed biochemistry WRKYAltered seed protein content 1022 (114-170) 1023 G2543 Seed proteincontent Seed biochemistry HB Altered seed protein content 1024 (31-991)1025 G264 Seed protein content Seed biochemistry HS Altered seed proteincontent 1026 (24-114) 1027 G32 Seed protein content Seed biochemistryAP2 Altered seed protein content 1028 (17-84) 1029 G436 Seed proteincontent Seed biochemistry HB Altered seed protein content 1030 (22-85)1031 G556 Seed protein content Seed biochemistry bZIP Altered seedprotein content 1032 (83-143) 1033 G1420 Seed protein content Seedbiochemistry WRKY Altered seed protein content 1034 (221-280) 1035 G1412Seed protein content Seed biochemistry NAC Altered seed protein content1036 (17-159) 1037 G738 Seed protein content Seed biochemistry Z-DofAltered seed protein content 1038 (351-393) 1039 G2426 Seed proteincontent Seed biochemistry MYB-(R1) Altered seed protein content 1040(14-114) R2R3 1041 G1524 Seed protein content Seed biochemistryRING/C3HC3 Altered seed protein content 1042 (49-110) 1043 G1243 Seedprotein content Seed biochemistry SWI/SNF Altered seed protein content1044 (216-609) 1045 G631 Seed protein content Seed biochemistry bZIPAltered seed protein content 1046 (TBD) 1047 G1909 Seed protein contentSeed biochemistry Z-Dof Altered seed protein content 1048 (23-51) 1049G1663 Seed protein content Seed biochemistry PCF Altered seed proteincontent 1050 (TBD) 1051 G1231 Seed protein content Seed biochemistryZ-C4HC3 Altered seed protein content 1052 (TBD) 1053 G227 Seed proteincontent Seed biochemistry MYB-(R1) Altered seed protein content 1054(13-112) R2R3 1055 G1842 Seed protein content Seed biochemistry MADSAltered seed protein content 1056 (2-57) 1057 G1505 Seed protein contentSeed biochemistry GATA/Zn Altered seed protein content 1058 (TBD) 1059G657 Seed protein content Seed biochemistry MYB-(R1) Altered seedprotein content 1060 (TBD) R2R3 1061 G1959 Seed protein content Seedbiochemistry GARP Altered seed protein content 1062 (46-97) 1063 G2180Seed protein content Seed biochemistry NAC Altered seed protein content1064 (7-156) 1065 G1817 Seed protein content Seed biochemistry PMRAltered seed protein content 1066 (47-331) 1067 G1649 Seed proteincontent Seed biochemistry HLH/MYC Altered seed protein content 1068(225-295) 1069 G2131 Seed protein content Seed biochemistry AP2 Alteredseed protein content 1070 (50-186, 112-183) 1071 G215 Seed proteincontent Seed biochemistry MYB-related Altered seed protein content 1072(TBD) 1073 G1508 Seed protein content Seed biochemistry GATA/Zn Alteredseed protein content 1074 (38-63) 1075 G2110 Seed protein content Seedbiochemistry WRKY Altered seed protein content 1076 (239-298) 1077 G2442Seed protein content Seed biochemistry RING/C3HC4 Altered seed proteincontent 1078 (220-246) 1079 G1051 Flowering time Flowering time bZIPLate flowering 1080 (189-250) 1081 G1052 Flowering time Flowering timebZIP Late flowering 1082 (201-261) 1083 G1079 Flowering Flowering BZIPT2Late flowering; altered 1084 (1-50) time; seed time; seed seed proteincontent protein biochemistry content 1085 G1335 Flowering FloweringZ-CLDSH Late flowering, slow 1086 (24-43, time time growth 131-144,185-203) 1087 G157 Flowering Flowering MAPS Altered flowering; 1088(2-57) time time significant overexpression delays flowering time 1089G1895 Flowering Flowering Z-Dof Late flowering 1090 (55-110) time time1091 G1900 Flowering Flowering Z-Dof Late flowering 1092 (54-106) timetime 1093 G2007 Flowering Flowering MYB-(R1) Late flowering; altered1094 (TBD) time; seed time; seed R2R3 seed protein content proteinbiochemistry content 1095 G214 Flowering time Flowering time MYB-relatedLate flowering 1096 (22-71) 1097 G2155 Flowering time Flowering timeAT-hook Late flowering 1098 (18-38) 1099 G234 Flowering Flowering MYB-Late flowering, small 1100 (14-115) time time (R1)R2R3 plant 1101 G361Flowering Flowering Z-C2H2 Late flowering 1102 (43-63) time time 1103G562 Flowering Flowering bZIP Late flowering 1104 (253-315) time time1105 G591 Flowering Flowering HLH/MYC Late flowering 1106 (143-240) timetime 1107 G8 Flowering Flowering AP2 Late flowering 1108 (151-217, timetime 243-296) 1109 G859 Flowering Flowering MADS Late flowering; altered1110 (TBD) time; seed time; seed seed protein content proteinbiochemistry content 1111 G878 Flowering time Flowering time WRKY Lateflowering 1112 (250-305, 415-475) 1113 G971 Flowering Flowering AP2 Lateflowering 1114 (120-186) time time 1115 G975 Flowering Flowering AP2Late flowering; 1116 (4-71) time; time; dev and glossy leavesmorphology: morph other 1117 G994 Flowering Flowering MYB- Lateflowering, small 1118 (14-123) time time (R1)R2R3 1119 G2347 FloweringFlowering SBP Late flowering, small 1120 (60-136) time time 1121 G2010Flowering Flowering SBP Late flowering 1122 (53-127) time time

TABLE 6 Genes, traits and utilities that affect plant characteristicsTranscription factor genes that Utility Trait Category Traits impacttraits Gene effect on: Resistance and Salt stress resistance G22; G196;G226; G303; G312; Germination rate, tolerance G325; G353; G482; G545;G801; survivability, yield; G867; G884; G922; G926; G1452; extendedgrowth G1794; G1820; G1836; G1843; range G1863; G2053; G2110; G2140;G2153; G2379; G2701; G2713; G2719; G2789 Osmotic stress G47; G175; G188;G303; G325; Germination rate, resistance G353; G489; G502; G526; G921;survivability, yield G922; G926; G1069; G1089; G1452; G1794; G1930;G2140; G2153; G2379; G2701; G2719; G2789; Cold stress resistance; G256;G394; G664; G864; G1322; Germination, cold germination G2130 growth,earlier planting Tolerance to freezing G303; G325; G353; G720; G912;Survivability, yield, G913; G1794; G2053; G2140; appearance, G2153;G2379; G2701; G2719; extended range G2789 Heat stress resistance G3;G464; G682; G864; G964; Germination, G1305; G1645; G2130 G2430 growth,later planting Drought, low humidity G303; G325; G353; G720; G912;Survivability, yield, resistance G926; G1452; G1794; G1820; extendedrange G1843; G2053; G2140; G2153; G2379; G2583; G2701; G2719; G2789Radiation resistance G1052 Survivability, vigor, appearance Decreasedherbicide G343; G2133; G2517 Resistant to sensitivity increasedherbicide use Increased herbicide G374; G877; G1519 Use as a herbicidesensitivity target Oxidative stress G477; G789; G1807; G2133; Improvedyield, G2517 appearance, reduced senescence Light response G183; G354;G375; G1062; Germination, G1322; G1331; G1488; G1494; growth, G1521;G1786; G1794; G2144; development, G2555; flowering time Development,Overall plant G24; G27; G31; G33; G47; G147; Vascular tissues,morphology architecture G156; G160; G182; G187; G195; lignin content;cell G196; G211; G221; G237; G280; wall content; G342; G352; G357; G358;G360; appearance G362; G364; G365; G367; G373; G377; G396; G431; G447;G479; G546; G546; G551; G578; G580; G596; G615; G617; G620; G625; G638;G658; G716; G725; G727; G730; G740; G770; G858; G865; G869; G872; G904;G910; G912; G920; G939; G963; G977; G979; G987; G988; G993; G1007;G1010; G1014; G1035; G1046; G1049; G1062; G1069; G1070; G1076; G1089;G1093; G1127; G1131; G1145; G1229; G1246; G1304; G1318; G1320; G1330;G1331; G1352; G1354; G1360; G1364; G1379; G1384; G1399; G1415; G1417;G1442; G1453; G1454; G1459; G1460; G1471; G1475; G1477; G1487; G1487;G1492; G1499; G1499; G1531; G1540; G1543; G1543; G1544; G1548; G1584;G1587; G1588; G1589; G1636; G1642; G1747; G1749; G1749; G1751; G1752;G1763; G1766; G1767; G1778; G1789; G1790; G1791; G1793; G1794; G1795;G1800; G1806; G1811; G1835; G1836; G1838; G1839; G1843; G1853; G1855;G1865; G1881; G1882; G1883; G1884; G1891; G1896; G1898; G1902; G1904;G1906; G1913; G1914; G1925; G1929; G1930; G1954; G1958; G1965; G1976;G2057; G2107; G2133; G2134; G2151; G2154; G2157; G2181; G2290; G2299;G2340; G2340; G2346; G2373; G2376; G2424; G2465; G2505; G2509; G2512;G2513; G2519; G2520; G2533; G2534; G2573; G2589; G2687; G2720; G2787;G2789; G2893 Size: increased stature G189; G1073; G1435; G2430 Size:reduced stature or G3; G5; G21; G23; G39; G165; Ornamental; smalldwarfism G184; G194; G258; G280; G340; stature provides G343; G353;G354; G362; G363; wind resistance; G370; G385; G396; G439; G440;creation of dwarf G447; G450; G550; G557; G599; varieties G636; G652;G670; G671; G674; G729; G760; G804; G831; G864; G884; G898; G900; G912;G913; G922; G932; G937; G939; G960; G962; G977; G991; G1000; G1008;G1020; G1023; G1053; G1067; G1075; G1137; G1181; G1198; G1228; G1266;G1267; G1275; G1277; G1309; G1311; G1314; G1317; G1322; G1323; G1326;G1332; G1334; G1367; G1381; G1382; G1386; G1421; G1488; G1494; G1537;G1545; G1560; G1586; G1641; G1652; G1655; G1671; G1750; G1756; G1757;G1782; G1786; G1794; G1839; G1845; G1879; G1886; G1888; G1933; G1939;G1943; G1944; G2011; G2094; G2115; G2130; G2132; G2144; G2145; G2147;G2156; G2294; G2313; G2344; G2431; G2510; G2517; G2521; G2893; G2893Fruit size and number G362 Biomass, yield, cotton boll fiber densityFlower structure, G47; G259; G353; G354; G671; Ornamental inflorescenceG732; G988; G1000; G1063; horticulture; G1140; G1326; G1449; G1543;production of G1560; G1587; G1645; G1947; saffron or other G2108; G2143;G2893 edible flowers Number and G225; G226; G247; G362; G585; Resistanceto pests development of G634; G676; G682; G1014; and desiccation;trichomes G1332; G1452; G1795; G2105 essential oil production Seed size,color, and G156; G450; G584; G652; G668; Yield number G858; G979; G1040;G1062; G1145; G1255; G1494; G1531; G1534; G1594; G2105; G2114; Rootdevelopment, G9; G1482; G1534; G1794; modifications G1852; G2053; G2136;G2140 Modifications to root G225; G226 Nutrient, water hairs uptake,pathogen resistance Apical dominance G559; G732; G1255; G1275;Ornamental G1411; G1488; G1635; G2452; horticulture G2509 Branchingpatterns G568; G988; G1548 Ornamental horticulture, knot reduction,improved windscreen Leaf shape, color, G375; G377; G428; G438; G447;Appealing shape or modifications G464; G557; G577; G599; G635; shinyleaves for G671; G674; G736; G804; G903; ornamental G977; G921; G922;G1038; agriculture, G1063; G1067; G1073; G1075; increased biomass G1146;G1152; G1198; G1267; or photosynthesis G1269; G1452; G1484; G1586;G1594; G1767; G1786; G1792; G1886; G2059; G2094; G2105; G2113; G2117;G2143; G2144; G2431; G2452; G2465; G2587; G2583; G2724; Silique G1134Ornamental Stem morphology G47; G438; G671; G748; G988; Ornamental;G1000 digestibility Shoot modifications G390; G391 Ornamental stembifurcations Disease, Pathogen Bacterial G211; G347; G367; G418; G525;Yield, appearance, Resistance G545; G578; G1049 survivability, extendedrange Fungal G19; G28; G28; G28; G147; Yield, appearance, G188; G207;G211; G237; G248; survivability, G278; G347; G367; G371; G378; extendedrange G409; G477; G545; G545; G558; G569; G578; G591; G594; G616; G789;G805; G812; G865; G869; G872; G881; G896; G940; G1047; G1049; G1064;G1084; G1196; G1255; G1266; G1363; G1514; G1756; G1792; G1792; G1792;G1792; G1880; G1919; G1919; G1927; G1927; G1936; G1936; G1950; G2069;G2130; G2380; G2380; G2555 Nutrients Increased tolerance to G255; G226;G1792 nitrogen-limited soils Increased tolerance to G419; G545; G561;G1946 phosphate-limited soils Increased tolerance to G561; G911potassium-limited soils Hormonal Hormone sensitivity G12; G546; G926;G760; G913; Seed dormancy, G926; G1062; G1069; G1095; drought tolerance;G1134; G1330; G1452; G1666; plant form, fruit G1820; G2140; G2789ripening Seed biochemistry Production of seed G214; G259; G490; G652;G748; Antioxidant activity, prenyl lipids, including G883; G1052; G1328;G1930; vitamin E tocopherol G2509; G2520 Production of seed G20Precursors for sterols human steroid hormones; cholesterol modulatorsProduction of seed G353; G484; G674; G1272; Defense againstglucosinolates G1506; G1897; G1946; G2113; insects; putative G2117;G2155; G2290; G2340 anticancer activity; undesirable in animal feedsModified seed oil G162; G162; G180; G192; G241; Vegetable oil contentG265; G286; G291; G427; G509; production; G519; G561; G567; G590; G818;increased caloric G849; G892; G961; G974; G1063; value for animal G1143;G1190; G1198; G1226; feeds; lutein content G1229; G1323; G1451; G1471;G1478; G1496; G1526; G1543; G1640; G1644; G1646; G1672; G1677; G1750;G1765; G1777; G1793; G1838; G1902; G1946; G1948; G2059; G2123; G2138;G2139; G2343; G2792; G2830 Modified seed oil G217; G504; G622; G778;G791; Heat stability, composition G861; G869; G938; G965; G1417;digestibility of seed G2192 oils Modified seed protein G162; G226; G241;G371; G427; Reduced caloric content G509; G567; G597; G732; G849; valuefor humans G865; G892; G963; G988; G1323; G1323; G1419; G1478; G1488;G1634; G1637; G1641; G1644; G1652; G1677; G1777; G1777; G1818; G1820;G1903; G1909; G1946; G1946; G1958; G2059; G2117; G2417; G2509 Leafbiochemistry Production of flavonoids G1666* Ornamental pigmentproduction; pathogen resistance; health benefits Production of leafG264; G353; G484; G652; G674; Defense against glucosinolates G681;G1069; G1198; G1322; insects; putative G1421; G1657; G1794; G1897;anticancer activity; G1946; G2115; G2117; G2144; undesirable in G2155;G2155; G2340; G2512; animal feeds G2520; G2552 Production of diterpenesG229 Induction of enzymes involved in alkaloid biosynthesis Productionof G546 Ornamental pigment anthocyanin Production of leaf G561; G2131;G2424 Precursors for phytosterols, inc. human steroid stigmastanol,hormones; campesterol cholesterol modulators Leaf fatty acid G214; G377;G861; G962; G975; Nutritional value; composition G987; G1266; G1337;G1399; increase in waxes G1465; G1512; G2136; G2147; for disease G2192resistance Production of leaf G214; G259; G280; G652; G987; Antioxidantactivity, prenyl lipids, including G1543; G2509; G2520 vitamin Etocopherol Biochemistry, Production of G229; G663 general miscellaneoussecondary metabolites Sugar, starch, G158; G211; G211; G237; G242; Fooddigestibility, hemicellulose G274; G598; G1012; G1266; hemicellulose &composition, G1309; G1309; G1641; G1765; pectin content; fiber G1865;G2094; G2094; G2589; content; plant G2589 tensile strength, woodquality, pathogen resistance, pulp production; tuber starch contentSugar sensing Plant response to sugars G26; G38; G43; G207; G218;Photosynthetic rate, G241; G254; G263; G308; G536; carbohydrate G567;G567; G680; G867; G912; accumulation, G956; G996; G1068; G1225; biomassproduction, G1314; G1314; G1337; G1759; source-sink G1804; G2153; G2379;relationships, senescence Growth, Plant growth rate and G447; G617;G674; G730; G917; Faster growth, Reproduction development G937; G1035;G1046; G1131; increased biomass G1425; G1452; G1459; G1492; or yield,improved G1589; G1652; G1879; G1943; appearance; delay in G2430; G2431;G2465; G2521 bolting Embryo development G167 Seed germination rate G979;G1792; G2130 Yield Plant, seedling vigor G561; G2346 Survivability,yield Senescence; cell death G571; G636; G878; G1050; Yield, appearance;G1463; G1749; G1944; G2130; response to G2155; G2340; G2383 pathogens;Modified fertility G39; G340; G439; G470; G559; Prevents or G615; G652;G671; G779; G962; minimizes escape of G977; G988; G1000; G1063; thepollen of GMOs G1067; G1075; G1266; G1311; G1321; G1326; G1367; G1386;G1421; G1453; G1471; G1453; G1560; G1594; G1635; G1750; G1947; G2011;G2094; G2113; G2115; G2130; G2143; G2147; G2294; G2510; G2893 Earlyflowering G147; G157; G180; G183; G183; Faster generation G184; G185;G208; G227; G294; time; synchrony of G390; G390; G390; G391; G391;flowering; potential G427; G427; G490; G565; G590; for introducing newG592; G720; G789; G865; G898; traits to single G898; G989; G989; G1037;variety G1037; G1142; G1225; G1225; G1226; G1242; G1305; G1305; G1380;G1380; G1480; G1480; G1488; G1494; G1545; G1545; G1649; G1706; G1760;G1767; G1767; G1820; G1841; G1841; G1842; G1843; G1843; G1946; G1946;G2010; G2030; G2030; G2144; G2144; G2295; G2295; G2347; G2348; G2348;G2373; G2373; G2509; G2509; G2555; G2555 Delayed flowering G8; G47;G192; G214; G234; Delayed time to G361; G362; G562; G568; G571; pollenproduction of G591; G680; G736; G748; G859; GMO plants; G878; G910;G912; G913; G971; synchrony of G994; G1051; G1052; G1073; flowering;increased G1079; G1335; G1435; G1452; yield G1478; G1789; G1804; G1865;G1865; G1895; G1900; G2007; G2133; G2155; G2291; G2465 Extendedflowering G1947 phase Flower and leaf G259; G353; G377; G580; G638Ornamental development G652; G858; G869; G917; G922; applications; G932;G1063; G1075; G1140; decreased fertility G1425; G1452; G1499; G1548;G1645; G1865; G1897; G1933; G2094; G2124; G2140; G2143; G2535; G2557Flower abscission G1897 Ornamental: longer retention of flowers *Whenco-expressed with G669 and G663Significance of Modified Plant Traits

Currently, the existence of a series of maturity groups for differentlatitudes represents a major barrier to the introduction of new valuabletraits. Any trait (e.g. disease resistance) has to be bred into each ofthe different maturity groups separately, a laborious and costlyexercise. The availability of single strain, which could be grown at anylatitude, would therefore greatly increase the potential for introducingnew traits to crop species such as soybean and cotton.

For many of the traits, listed in Table 6 and below, that may beconferred to plants, a single transcription factor gene may be used toincrease or decrease, advance or delay, or improve or prove deleteriousto a given trait. For example, overexpression of a transcription factorgene that naturally occurs in a plant may cause early flowering relativeto non-transformed or wild-type plants. By knocking out the gene, orsuppressing the gene (with, for example, antisense suppression) theplant may experience delayed flowering. Similarly, overexpressing orsuppressing one or more genes can impart significant differences inproduction of plant products, such as different fatty acid ratios. Thus,suppressing a gene that causes a plant to be more sensitive to cold mayimprove a plant's tolerance of cold.

Salt stress resistance. Soil salinity is one of the more importantvariables that determines where a plant may thrive. Salinity isespecially important for the successful cultivation of crop plants,particular in many parts of the world that have naturally high soil saltconcentrations, or where the soil has been over-utilized. Thus,presently disclosed transcription factor genes that provide increasedsalt tolerance during germination, the seedling stage, and throughout aplant's life cycle would find particular value for impartingsurvivability and yield in areas where a particular crop would notnormally prosper.

Osmotic stress resistance. Presently disclosed transcription factorgenes that confer resistance to osmotic stress may increase germinationrate under adverse conditions, which could impact survivability andyield of seeds and plants.

Cold stress resistance. The potential utility of presently disclosedtranscription factor genes that increase tolerance to cold is to conferbetter germination and growth in cold conditions. The germination ofmany crops is very sensitive to cold temperatures. Genes that wouldallow germination and seedling vigor in the cold would have highlysignificant utility in allowing seeds to be planted earlier in theseason with a high rate of survivability. Transcription factor genesthat confer better survivability in cooler climates allow a grower tomove up planting time in the spring and extend the growing seasonfurther into autumn for higher crop yields.

Tolerance to freezing. The presently disclosed transcription factorgenes that impart tolerance to freezing conditions are useful forenhancing the survivability and appearance of plants conditions orconditions that would otherwise cause extensive cellular damage. Thus,germination of seeds and survival may take place at temperaturessignificantly below that of the mean temperature required forgermination of seeds and survival of non-transformed plants. As withsalt tolerance, this has the added benefit of increasing the potentialrange of a crop plant into regions in which it would otherwise succumb.Cold tolerant transformed plants may also be planted earlier in thespring or later in autumn, with greater success than withnon-transformed plants.

Heat stress tolerance. The germination of many crops is also sensitiveto high temperatures. Presently disclosed transcription factor genesthat provide increased heat tolerance are generally useful in producingplants that germinate and grow in hot conditions, may find particularuse for crops that are planted late in the season, or extend the rangeof a plant by allowing growth in relatively hot climates.

Drought, low humidity tolerance. Strategies that allow plants to survivein low water conditions may include, for example, reduced surface areaor surface oil or wax production. A number of presently disclosedtranscription factor genes increase a plant's tolerance to low waterconditions and provide the benefits of improved survivability, increasedyield and an extended geographic and temporal planting range.

Radiation resistance. Presently disclosed transcription factor geneshave been shown to increase lutein production. Lutein, like otherxanthophylls such as zeaxanthin and violaxanthin, are important in theprotection of plants against the damaging effects of excessive light.Lutein contributes, directly or indirectly, to the rapid rise ofnon-photochemical quenching in plants exposed to high light. Increasedtolerance of field plants to visible and ultraviolet light impactssurvivability and vigor, particularly for recent transplants. Alsoaffected are the yield and appearance of harvested plants or plantparts. Crop plants engineered with presently disclosed transcriptionfactor genes that cause the plant to produce higher levels of luteintherefore would have improved photoprotection, leading to less oxidativedamage and increase vigor, survivability and higher yields under highlight and ultraviolet light conditions.

Decreased herbicide sensitivity. Presently disclosed transcriptionfactor genes that confer resistance or tolerance to herbicides (e.g.,glyphosate) may find use in providing means to increase herbicideapplications without detriment to desirable plants. This would allow forthe increased use of a particular herbicide in a local environment, withthe effect of increased detriment to undesirable species and less harmto transgenic, desirable cultivars.

Increased herbicide sensitivity. Knockouts of a number of the presentlydisclosed transcription factor genes have been shown to be lethal todeveloping embryos. Thus, these genes are potentially useful asherbicide targets.

Oxidative stress. In plants, as in all living things, abiotic and bioticstresses induce the formation of oxygen radicals, including superoxideand peroxide radicals. This has the effect of accelerating senescence,particularly in leaves, with the resulting loss of yield and adverseeffect on appearance. Generally, plants that have the highest level ofdefense mechanisms, such as, for example, polyunsaturated moieties ofmembrane lipids, are most likely to thrive under conditions thatintroduce oxidative stress (e.g., high light, ozone, water deficit,particularly in combination). Introduction of the presently disclosedtranscription factor genes that increase the level of oxidative stressdefense mechanisms would provide beneficial effects on the yield andappearance of plants. One specific oxidizing agent, ozone, has beenshown to cause significant foliar injury, which impacts yield andappearance of crop and ornamental plants. In addition to reduced foliarinjury that would be found in ozone resistant plant created bytransforming plants with some of the presently disclosed transcriptionfactor genes, the latter have also been shown to have increasedchlorophyll fluorescence (Yu-Sen Chang et al. Bot. Bull. Acad. Sin.(2001) 42: 265-272).

Heavy metal tolerance. Heavy metals such as lead, mercury, arsenic,chromium and others may have a significant adverse impact on plantrespiration. Plants that have been transformed with presently disclosedtranscription factor genes that confer improved resistance to heavymetals, through, for example, sequestering or reduced uptake of themetals will show improved vigor and yield in soils with relatively highconcentrations of these elements. Conversely, transgenic transcriptionfactors may also be introduced into plants to confer an increase inheavy metal uptake, which may benefit efforts to clean up contaminatedsoils.

Light response. Presently disclosed transcription factor genes thatmodify a plant's response to light may be useful for modifying a plant'sgrowth or development, for example, photomorphogenesis in poor light, oraccelerating flowering time in response to various light intensities,quality or duration to which a non-transformed plant would not similarlyrespond. Examples of such responses that have been demonstrated includeleaf number and arrangement, and early flower bud appearances.

Overall plant architecture. Several presently disclosed transcriptionfactor genes have been introduced into plants to alter numerous aspectsof the plant's morphology. For example, it has been demonstrated that anumber of transcription factors may be used to manipulate branching,such as the means to modify lateral branching, a possible application inthe forestry industry. Transgenic plants have also been produced thathave altered cell wall content, lignin production, flower organ number,or overall shape of the plants. Presently disclosed transcription factorgenes transformed into plants may be used to affect plant morphology byincreasing or decreasing internode distance, both of which may beadvantageous under different circumstances. For example, for fast growthof woody plants to provide more biomass, or fewer knots, increasedinternode distances are generally desirable. For improved wind screeningof shrubs or trees, or harvesting characteristics of, for example,members of the Gramineae family, decreased internode distance may beadvantageous. These modifications would also prove useful in theornamental horticulture industry for the creation of unique phenotypiccharacteristics of ornamental plants.

Increased stature. For some ornamental plants, the ability to providelarger varieties may be highly desirable. For many plants, including tfruit-bearing trees or trees and shrubs that serve as view or windscreens, increased stature provides obvious benefits. Crop species mayalso produce higher yields on larger cultivars.

Reduced stature or dwarfism. Presently disclosed transcription factorgenes that decrease plant stature can be used to produce plants that aremore resistant to damage by wind and rain, or more resistant to heat orlow humidity or water deficit. Dwarf plants are also of significantinterest to the ornamental horticulture industry, and particularly forhome garden applications for which space availability may be limited.

Fruit size and number. Introduction of presently disclosed transcriptionfactor genes that affect fruit size will have desirable impacts on fruitsize and number, which may comprise increases in yield for fruit crops,or reduced fruit yield, such as when vegetative growth is preferred(e.g., with bushy ornamentals, or where fruit is undesirable, as withornamental olive trees).

Flower structure inflorescence and development. Presently disclosedtransgenic transcription factors have been used to create plants withlarger flowers or arrangements of flowers that are distinct fromwild-type or non-transformed cultivars. This would likely have the mostvalue for the ornamental horticulture industry, where larger flowers orinteresting presentations generally are preferred and command thehighest prices. Flower structure may have advantageous effects onfertility, and could be used, for example, to decrease fertility by theabsence, reduction or screening of reproductive components. Oneinteresting application for manipulation of flower structure, forexample, by introduced transcription factors could be in the increasedproduction of edible flowers or flower parts, including saffron, whichis derived from the stigmas of Crocus sativus.

Number and development of trichomes. Several presently disclosedtranscription factor genes have been used to modify trichome number andamount of trichome products in plants. Trichome glands on the surface ofmany higher plants produce and secrete exudates that give protectionfrom the elements and pests such as insects, microbes and herbivores.These exudates may physically immobilize insects and spores, may beinsecticidal or ant-microbial or they may act as allergens or irritantsto protect against herbivores. Trichomes have also been suggested todecrease transpiration by decreasing leaf surface air flow, and byexuding chemicals that protect the leaf from the sun.

Seed size, color and number. The introduction of presently disclosedtranscription factor genes into plants that alter the size or number ofseeds may have a significant impact on yield, both when the product isthe seed itself, or when biomass of the vegetative portion of the plantis increased by reducing seed production. In the case of fruit products,it is often advantageous to modify a plant to have reduced size ornumber of seeds relative to non-transformed plants to provide seedlessor varieties with reduced numbers or smaller seeds. Presently disclosedtranscription factor genes have also been shown to affect seed size,including the development of larger seeds. Seed size, in addition toseed coat integrity, thickness and permeability, seed water content andby a number of other components including antioxidants andoligosaccharides, may affect seed longevity in storage. This would be animportant utility when the seed of a plant is the harvested crops, aswith, for example, peas, beans, nuts, etc. Presently disclosedtranscription factor genes have also been used to modify seed color,which could provide added appeal to a seed product.

Root development, modifications. By modifying the structure ordevelopment of roots by transforming into a plant one or more of thepresently disclosed transcription factor genes, plants may be producedthat have the capacity to thrive in otherwise unproductive soils. Forexample, grape roots that extend further into rocky soils, or thatremain viable in waterlogged soils, would increase the effectiveplanting range of the crop. It may be advantageous to manipulate a plantto produce short roots, as when a soil in which the plant will begrowing is occasionally flooded, or when pathogenic fungi ordisease-causing nematodes are prevalent.

Modifications to root hairs. Presently disclosed transcription factorgenes that increase root hair length or number potentially could be usedto increase root growth or vigor, which might in turn allow better plantgrowth under adverse conditions such as limited nutrient or wateravailability.

Apical dominance. The modified expression of presently disclosedtranscription factors that control apical dominance could be used inornamental horticulture, for example, to modify plant architecture.

Branching patterns. Several presently disclosed transcription factorgenes have been used to manipulate branching, which could providebenefits in the forestry industry. For example, reduction in theformation of lateral branches could reduce knot formation. Conversely,increasing the number of lateral branches could provide utility when aplant is used as a windscreen, or may also provide ornamentaladvantages.

Leaf shape, color and modifications. It has been demonstrated inlaboratory experiments that overexpression of some of the presentlydisclosed transcription factors produced marked effects on leafdevelopment. At early stages of growth, these transgenic seedlingsdeveloped narrow, upward pointing leaves with long petioles, possiblyindicating a disruption in circadian-clock controlled processes ornyctinastic movements. Other transcription factor genes can be used toincrease plant biomass; large size would be useful in crops where thevegetative portion of the plant is the marketable portion.

Siliques. Genes that later silique conformation in brassicates may beused to modify fruit ripening processes in brassicates and other plants,which may positively affect seed or fruit quality.

Stem morphology and shoot modifications. Laboratory studies havedemonstrated that introducing several of the presently disclosedtranscription factor genes into plants can cause stem bifurcations inshoots, in which the shoot meristems split to form two or three separateshoots. This unique appearance would be desirable in ornamentalapplications.

Diseases, pathogens and pests. A number of the presently disclosedtranscription factor genes have been shown to or are likely to conferresistance to various plant diseases, pathogens and pests. The offendingorganisms include fungal pathogens Fusarium oxysporum, Botrytis cinerea,Sclerotinia sclerotiorum, and Erysiphe orontii. Bacterial pathogens towhich resistance may be conferred include Pseudomonas syringae. Otherproblem organisms may potentially include nematodes, mollicutes,parasites, or herbivorous arthropods. In each case, one or moretransformed transcription factor genes may provide some benefit to theplant to help prevent or overcome infestation. The mechanisms by whichthe transcription factors work could include increasing surface waxes oroils, surface thickness, local senescence, or the activation of signaltransduction pathways that regulate plant defense in response to attacksby herbivorous pests (including, for example, protease inhibitors).

Increased tolerance of plants to nutrient-limited soils. Presentlydisclosed transcription factor genes introduced into plants may providethe means to improve uptake of essential nutrients, includingnitrogenous compounds, phosphates, potassium, and trace minerals. Theeffect of these modifications is to increase the seedling germinationand range of ornamental and crop plants. The utilities of presentlydisclosed transcription factor genes conferring tolerance to conditionsof low nutrients also include cost savings to the grower by reducing theamounts of fertilizer needed, environmental benefits of reducedfertilizer runoff; and improved yield and stress tolerance. In addition,this gene could be used to alter seed protein amounts and/or compositionthat could impact yield as well as the nutritional value and productionof various food products.

Hormone sensitivity. One or more of the presently disclosedtranscription factor genes have been shown to affect plant abscisic acid(ABA) sensitivity. This plant hormone is likely the most importanthormone in mediating the adaptation of a plant to stress. For example,ABA mediates conversion of apical meristems into dormant buds. Inresponse to increasingly cold conditions, the newly developing leavesgrowing above the meristem become converted into stiff bud scales thatclosely wrap the meristem and protect it from mechanical damage duringwinter. ABA in the bud also enforces dormancy; during premature warmspells, the buds are inhibited from sprouting. Bud dormancy iseliminated after either a prolonged cold period of cold or a significantnumber of lengthening days. Thus, by affecting ABA sensitivity,introduced transcription factor genes may affect cold sensitivity andsurvivability. ABA is also important in protecting plants from droughttolerance.

Several other of the present transcription factor genes have been usedto manipulate ethylene signal transduction and response pathways. Thesegenes can thus be used to manipulate the processes influenced byethylene, such as seed germination or fruit ripening, and to improveseed or fruit quality.

Production of seed and leaf prenyl lipids, including tocopherol. Prenyllipids play a role in anchoring proteins in membranes or membranousorganelles. Thus modifying the prenyl lipid content of seeds and leavescould affect membrane integrity and function. A number of presentlydisclosed transcription factor genes have been shown to modify thetocopherol composition of plants. Tocopherols have both anti-oxidant andvitamin E activity.

Production of seed and leaf phytosterols: Presently disclosedtranscription factor genes that modify levels of phytosterols in plantsmay have at least two utilities. First, phytosterols are an importantsource of precursors for the manufacture of human steroid hormones.Thus, regulation of transcription factor expression or activity couldlead to elevated levels of important human steroid precursors forsteroid semi-synthesis. For example, transcription factors that causeelevated levels of campesterol in leaves, or sitosterols andstigmasterols in seed crops, would be useful for this purpose.Phytosterols and their hydrogenated derivatives phytostanols also haveproven cholesterol-lowering properties, and transcription factor genesthat modify the expression of these compounds in plants would thusprovide health benefits.

Production of seed and leaf glucosinolates. Some glucosinolates haveanti-cancer activity; thus, increasing the levels or composition ofthese compounds by introducing several of the presently disclosedtranscription factors might be of interest from a nutraceuticalstandpoint. (3) Glucosinolates form part of a plants natural defenseagainst insects. Modification of glucosinolate composition or quantitycould therefore afford increased protection from predators. Furthermore,in edible crops, tissue specific promoters might be used to ensure thatthese compounds accumulate specifically in tissues, such as theepidermis, which are not taken for consumption.

Modified seed oil content. The composition of seeds, particularly withrespect to seed oil amounts and/or composition, is very important forthe nutritional value and production of various food and feed products.Several of the presently disclosed transcription factor genes in seedlipid saturation that alter seed oil content could be used to improvethe heat stability of oils or to improve the nutritional quality of seedoil, by, for example, reducing the number of calories in seed,increasing the number of calories in animal feeds, or altering the ratioof saturated to unsaturated lipids comprising the oils.

Seed and leaf fatty acid composition. A number of the presentlydisclosed transcription factor genes have been shown to alter the fattyacid composition in plants, and seeds in particular. This modificationmay find particular value for improving the nutritional value of, forexample, seeds or whole plants. Dietary fatty acids ratios have beenshown to have an effect on, for example, bone integrity and remodeling(see, for example, Weiler, H. A., Pediatr Res (2000) 47:5 692-697). Theratio of dietary fatty acids may alter the precursor pools of long-chainpolyunsaturated fatty acids that serve as precursors for prostaglandinsynthesis. In mammalian connective tissue, prostaglandins serve asimportant signals regulating the balance between resorption andformation in bone and cartilage. Thus dietary fatty acid ratios alteredin seeds may affect the etiology and outcome of bone loss.

Modified seed protein content. As with seed oils, the composition ofseeds, particularly with respect to protein amounts and/or composition,is very important for the nutritional value and production of variousfood and feed products. A number of the presently disclosedtranscription factor genes modify the protein concentrations in seedswould provide nutritional benefits, and may be used to prolong storage,increase seed pest or disease resistance, or modify germination rates.

Production of flavonoids in leaves and other plant parts. Expression ofpresently disclosed transcription factor genes that increase flavonoidproduction in plants, including anthocyanins and condensed tannins, maybe used to alter in pigment production for horticultural purposes, andpossibly increasing stress resistance. Flavonoids have antimicrobialactivity and could be used to engineer pathogen resistance. Severalflavonoid compounds have health promoting effects such as the inhibitionof tumor growth and cancer, prevention of bone loss and the preventionof the oxidation of lipids. Increasing levels of condensed tannins,whose biosynthetic pathway is shared with anthocyanin biosynthesis, inforage legumes is an important agronomic trait because they preventpasture bloat by collapsing protein foams within the rumen. For a reviewon the utilities of flavonoids and their derivatives, refer to Dixon etal. (1999) Trends Plant Sci. 4:394-400.

Production of diterpenes in leaves and other plant parts. Depending onthe plant species, varying amounts of diverse secondary biochemicals(often lipophilic terpenes) are produced and exuded or volatilized bytrichomes. These exotic secondary biochemicals, which are relativelyeasy to extract because they are on the surface of the leaf, have beenwidely used in such products as flavors and aromas, drugs, pesticidesand cosmetics. Thus, the overexpression of genes that are used toproduce diterpenes in plants may be accomplished by introducingtranscription factor genes that induce said overexpression. One class ofsecondary metabolites, the diterpenes, can effect several biologicalsystems such as tumor progression, prostaglandin synthesis and tissueinflammation. In addition, diterpenes can act as insect pheromones,termite allomones, and can exhibit neurotoxic, cytotoxic and antimitoticactivities. As a result of this functional diversity, diterpenes havebeen the target of research several pharmaceutical ventures. In mostcases where the metabolic pathways are impossible to engineer,increasing trichome density or size on leaves may be the only way toincrease plant productivity.

Production of anthocyanin in leaves and other plant parts. Severalpresently disclosed transcription factor genes can be used to alteranthocyanin production in numerous plant species. The potentialutilities of these genes include alterations in pigment production forhorticultural purposes, and possibly increasing stress resistance incombination with another transcription factor.

Production of miscellaneous secondary metabolites. Microarray datasuggests that flux through the aromatic amino acid biosynthetic pathwaysand primary and secondary metabolite biosynthetic pathways areup-regulated. Presently disclosed transcription factors have been shownto be involved in regulating alkaloid biosynthesis, in part byup-regulating the enzymes indole-3-glycerol phosphatase andstrictosidine synthase. Phenylalanine ammonia lyase, chalcone synthaseand trans-cinnamate mono-oxygenase are also induced, and are involved inphenylpropenoid biosynthesis.

Sugar, starch, hemicellulose composition. Overexpression of thepresently disclosed transcription factors that affect sugar contentresulted in plants with altered leaf insoluble sugar content.Transcription factors that alter plant cell wall composition haveseveral potential applications including altering food digestibility,plant tensile strength, wood quality, pathogen resistance and in pulpproduction. The potential utilities of a gene involved inglucose-specific sugar sensing are to alter energy balance,photosynthetic rate, carbohydrate accumulation, biomass production,source-sink relationships, and senescence.

Hemicellulose is not desirable in paper pulps because of its lack ofstrength compared with cellulose. Thus modulating the amounts ofcellulose vs. hemicellulose in the plant cell wall is desirable for thepaper/lumber industry. Increasing the insoluble carbohydrate content invarious fruits, vegetables, and other edible consumer products willresult in enhanced fiber content. Increased fiber content would not onlyprovide health benefits in food products, but might also increasedigestibility of forage crops. In addition, the hemicellulose and pectincontent of fruits and berries affects the quality of jam and catsup madefrom them. Changes in hemicellulose and pectin content could result in asuperior consumer product.

Plant response to sugars and sugar composition. In addition to theirimportant role as an energy source and structural component of the plantcell, sugars are central regulatory molecules that control severalaspects of plant physiology, metabolism and development. It is thoughtthat this control is achieved by regulating gene expression and, inhigher plants, sugars have been shown to repress or activate plant genesinvolved in many essential processes such as photosynthesis, glyoxylatemetabolism, respiration, starch and sucrose synthesis and degradation,pathogen response, wounding response, cell cycle regulation,pigmentation, flowering and senescence. The mechanisms by which sugarscontrol gene expression are not understood.

Because sugars are important signaling molecules, the ability to controleither the concentration of a signaling sugar or how the plant perceivesor responds to a signaling sugar could be used to control plantdevelopment, physiology or metabolism. For example, the flux of sucrose(a disaccharide sugar used for systemically transporting carbon andenergy in most plants) has been shown to affect gene expression andalter storage compound accumulation in seeds. Manipulation of thesucrose signaling pathway in seeds may therefore cause seeds to havemore protein, oil or carbohydrate, depending on the type ofmanipulation. Similarly, in tubers, sucrose is converted to starch whichis used as an energy store. It is thought that sugar signaling pathwaysmay partially determine the levels of starch synthesized in the tubers.The manipulation of sugar signaling in tubers could lead to tubers witha higher starch content.

Thus, the presently disclosed transcription factor genes that manipulatethe sugar signal transduction pathway may lead to altered geneexpression to produce plants with desirable traits. In particular,manipulation of sugar signal transduction pathways could be used toalter source-sink relationships in seeds, tubers, roots and otherstorage organs leading to increase in yield.

Plant growth rate and development. A number of the presently disclosedtranscription factor genes have been shown to have significant effectson plant growth rate and development. These observations have included,for example, more rapid or delayed growth and development ofreproductive organs. This would provide utility for regions with shortor long growing seasons, respectively. Accelerating plant growth wouldalso improve early yield or increase biomass at an earlier stage, whensuch is desirable (for example, in producing forestry products).

Embryo development. Presently disclosed transcription factor genes thatalter embryo development has been used to alter seed protein and oilamounts and/or composition which is very important for the nutritionalvalue and production of various food products. Seed shape and seed coatmay also be altered by these genes, which may provide for improvedstorage stability.

Seed germination rate. A number of the presently disclosed transcriptionfactor genes have been shown to modify seed germination rate, includingwhen the seeds are in conditions normally unfavorable for germination(e.g., cold, heat or salt stress, or in the presence of ABA), and maythus be used to modify and improve germination rates under adverseconditions.

Plant, seedling vigor. Seedlings transformed with presently disclosedtranscription factors have been shown to possess larger cotyledons andappeared somewhat more advanced than control plants. This indicates thatthe seedlings developed more rapidly that the control plants. Rapidseedling development is likely to reduce loss due to diseasesparticularly prevalent at the seedling stage (e.g., damping off) and isthus important for survivability of plants germinating in the field orin controlled environments.

Senescence, cell death. Presently disclosed transcription factor genesmay be used to alter senescence responses in plants. Although leafsenescence is thought to be an evolutionary adaptation to recyclenutrients, the ability to control senescence in an agricultural settinghas significant value. For example, a delay in leaf senescence in somemaize hybrids is associated with a significant increase in yields and adelay of a few days in the senescence of soybean plants can have a largeimpact on yield. Delayed flower senescence may also generate plants thatretain their blossoms longer and this may be of potential interest tothe ornamental horticulture industry.

Modified fertility. Plants that overexpress a number of the presentlydisclosed transcription factor genes have been shown to possess reducedfertility. This could be a desirable trait, as it could be exploited toprevent or minimize the escape of the pollen of genetically modifiedorganisms (GMOs) into the environment.

Early and delayed flowering. Presently disclosed transcription factorgenes that accelerate flowering could have valuable applications in suchprograms since they allow much faster generation times. In a number ofspecies, for example, broccoli, cauliflower, where the reproductiveparts of the plants constitute the crop and the vegetative tissues arediscarded, it would be advantageous to accelerate time to flowering.Accelerating flowering could shorten crop and tree breeding programs.Additionally, in some instances, a faster generation time might allowadditional harvests of a crop to be made within a given growing season.A number of Arabidopsis genes have already been shown to accelerateflowering when constitutively expressed. These include LEAFY, APETALA1and CONSTANS (Mandel, M. et al., 1995, Nature 377, 522-524; Weigel, D.and Nilsson, O., 1995, Nature 377, 495-500; Simon et al., 1996, Nature384, 59-62).

By regulating the expression of potential flowering using induciblepromoters, flowering could be triggered by application of an inducerchemical. This would allow flowering to be synchronized across a cropand facilitate more efficient harvesting. Such inducible systems couldalso be used to tune the flowering of crop varieties to differentlatitudes. At present, species such as soybean and cotton are availableas a series of maturity groups that are suitable for different latitudeson the basis of their flowering time (which is governed by day-length).A system in which flowering could be chemically controlled would allow asingle high-yielding northern maturity group to be grown at anylatitude. In southern regions such plants could be grown for longer,thereby increasing yields, before flowering was induced. In morenorthern areas, the induction would be used to ensure that the cropflowers prior to the first winter frosts.

In a sizeable number of species, for example, root crops, where thevegetative parts of the plants constitute the crop and the reproductivetissues are discarded, it would be advantageous to delay or preventflowering. Extending vegetative development with presently disclosedtranscription factor genes could thus bring about large increases inyields. Prevention of flowering might help maximize vegetative yieldsand prevent escape of genetically modified organism (GMO) pollen.

Extended flowering phase. Presently disclosed transcription factors thatextend flowering time have utility in engineering plants withlonger-lasting flowers for the horticulture industry, and for extendingthe time in which the plant is fertile.

Flower and leaf development. Presently disclosed transcription factorgenes have been used to modify the development of flowers and leaves.This could be advantageous in the development of new ornamentalcultivars that present unique configurations. In addition, some of thesegenes have been shown to reduce a plant's fertility, which is alsouseful for helping to prevent development of pollen of GMOs.

Flower abscission. Presently disclosed transcription factor genesintroduced into plants have been used to retain flowers for longerperiods. This would provide a significant benefit to the ornamentalindustry, for both cut flowers and woody plant varieties (of, forexample, maize), as well as have the potential to lengthen the fertileperiod of a plant, which could positively impact yield and breedingprograms.

A listing of specific effects and utilities that the presently disclosedtranscription factor genes have on plants, as determined by directobservation and assay analysis, is provided in Table 5.

XVI. ANTISENSE AND CO-SUPPRESSION

In addition to expression of the nucleic acids of the invention as genereplacement or plant phenotype modification nucleic acids, the nucleicacids are also useful for sense and anti-sense suppression ofexpression, e.g., to down-regulate expression of a nucleic acid of theinvention, e.g., as a further mechanism for modulating plant phenotype.That is, the nucleic acids of the invention, or subsequences oranti-sense sequences thereof, can be used to block expression ofnaturally occurring homologous nucleic acids. A variety of sense andanti-sense technologies are known in the art, e.g., as set forth inLichtenstein and Nellen (1997) Antisense Technology: A PracticalApproach IRL Press at Oxford University Press, Oxford, U.K. In general,sense or anti-sense sequences are introduced into a cell, where they areoptionally amplified, e.g., by transcription. Such sequences includeboth simple oligonucleotide sequences and catalytic sequences such asribozymes.

For example, a reduction or elimination of expression (i.e., a“knock-out”) of a transcription factor or transcription factor homologuepolypeptide in a transgenic plant, e.g., to modify a plant trait, can beobtained by introducing an antisense construct corresponding to thepolypeptide of interest as a cDNA. For antisense suppression, thetranscription factor or homologue cDNA is arranged in reverseorientation (with respect to the coding sequence) relative to thepromoter sequence in the expression vector. The introduced sequence neednot be the full length cDNA or gene, and need not be identical to thecDNA or gene found in the plant type to be transformed. Typically, theantisense sequence need only be capable of hybridizing to the targetgene or RNA of interest. Thus, where the introduced sequence is ofshorter length, a higher degree of homology to the endogenoustranscription factor sequence will be needed for effective antisensesuppression. While antisense sequences of various lengths can beutilized, preferably, the introduced antisense sequence in the vectorwill be at least 30 nucleotides in length, and improved antisensesuppression will typically be observed as the length of the antisensesequence increases. Preferably, the length of the antisense sequence inthe vector will be greater than 100 nucleotides. Transcription of anantisense construct as described results in the production of RNAmolecules that are the reverse complement of mRNA molecules transcribedfrom the endogenous transcription factor gene in the plant cell.

Suppression of endogenous transcription factor gene expression can alsobe achieved using a ribozyme. Ribozymes are RNA molecules that possesshighly specific endoribonuclease activity. The production and use ofribozymes are disclosed in U.S. Pat. No. 4,987,071 and U.S. Pat. No.5,543,508. Synthetic ribozyme sequences including antisense RNAs can beused to confer RNA cleaving activity on the antisense RNA, such thatendogenous mRNA molecules that hybridize to the antisense RNA arecleaved, which in turn leads to an enhanced antisense inhibition ofendogenous gene expression.

Vectors in which RNA encoded by a transcription factor or transcriptionfactor homologue cDNA is over-expressed can also be used to obtainco-suppression of a corresponding endogenous gene, e.g., in the mannerdescribed in U.S. Pat. No. 5,231,020 to Jorgensen. Such co-suppression(also termed sense suppression) does not require that the entiretranscription factor cDNA be introduced into the plant cells, nor doesit require that the introduced sequence be exactly identical to theendogenous transcription factor gene of interest. However, as withantisense suppression, the suppressive efficiency will be enhanced asspecificity of hybridization is increased, e.g., as the introducedsequence is lengthened, and/or as the sequence similarity between theintroduced sequence and the endogenous transcription factor gene isincreased.

Vectors expressing an untranslatable form of the transcription factormRNA, e.g., sequences comprising one or more stop codon, or nonsensemutation) can also be used to suppress expression of an endogenoustranscription factor, thereby reducing or eliminating it's activity andmodifying one or more traits. Methods for producing such constructs aredescribed in U.S. Pat. No. 5,583,021. Preferably, such constructs aremade by introducing a premature stop codon into the transcription factorgene. Alternatively, a plant trait can be modified by gene silencingusing double-strand RNA (Sharp (1999) Genes and Development 13:139-141).Another method for abolishing the expression of a gene is byinsertion mutagenesis using the T-DNA of Agrobacterium tumefaciens.After generating the insertion mutants, the mutants can be screened toidentify those containing the insertion in a transcription factor ortranscription factor homologue gene. Plants containing a singletransgene insertion event at the desired gene can be crossed to generatehomozygous plants for the mutation. Such methods are well known to thoseof skill in the art. (See for example Koncz et al. (1992) Methods inArabidopsis Research World Scientific.)

Alternatively, a plant phenotype can be altered by eliminating anendogenous gene, such as a transcription factor or transcription factorhomologue, e.g., by homologous recombination (Kempin et al. (1997)Nature 389:802-803).

A plant trait can also be modified by using the Cre-lox system (forexample, as described in U.S. Pat. No. 5,658,772). A plant genome can bemodified to include first and second lox sites that are then contactedwith a Cre recombinase. If the lox sites are in the same orientation,the intervening DNA sequence between the two sites is excised. If thelox sites are in the opposite orientation, the intervening sequence isinverted.

The polynucleotides and polypeptides of this invention can also beexpressed in a plant in the absence of an expression cassette bymanipulating the activity or expression level of the endogenous gene byother means. For example, by ectopically expressing a gene by T-DNAactivation tagging (Ichikawa et al. (1997) Nature 390 698-701; Kakimotoet al. (1996) Science 274: 982-985). This method entails transforming aplant with a gene tag containing multiple transcriptional enhancers andonce the tag has inserted into the genome, expression of a flanking genecoding sequence becomes deregulated. In another example, thetranscriptional machinery in a plant can be modified so as to increasetranscription levels of a polynucleotide of the invention (See, e.g.,PCT Publications WO 96/06166 and WO 98/53057 which describe themodification of the DNA-binding specificity of zinc finger proteins bychanging particular amino acids in the DNA-binding motif).

The transgenic plant can also include the machinery necessary forexpressing or altering the activity of a polypeptide encoded by anendogenous gene, for example by altering the phosphorylation state ofthe polypeptide to maintain it in an activated state.

Transgenic plants (or plant cells, or plant explants, or plant tissues)incorporating the polynucleotides of the invention and/or expressing thepolypeptides of the invention can be produced by a variety of wellestablished techniques as described above. Following construction of avector, most typically an expression cassette, including apolynucleotide, e.g., encoding a transcription factor or transcriptionfactor homologue, of the invention, standard techniques can be used tointroduce the polynucleotide into a plant, a plant cell, a plant explantor a plant tissue of interest. Optionally, the plant cell, explant ortissue can be regenerated to produce a transgenic plant.

The plant can be any higher plant, including gymnosperms,monocotyledonous and dicotyledenous plants. Suitable protocols areavailable for Leg minosae (alfalfa, soybean, clover, etc.), Umbelliferae(carrot, celery, parsnip), Cr ciferae (cabbage, radish, rapeseed,broccoli, etc.), Curcurbitaceae (melons and cucumber), Gramineae (wheat,corn, rice, barley, millet, etc.), Solanaceae (potato, tomato, tobacco,peppers, etc.), and various other crops. See protocols described inAmmirato et al. (1984) Handbook of Plant Cell Culture-Crop Species,Macmillan Publ. Co. Shimamoto et al. (1989) Nature 338:274-276; Fromm etal. (1990) Bio/Technology 8:833-839; and Vasil et al. (1990)Bio/Technology 8:429-434.

Transformation and regeneration of both monocotyledonous anddicotyledonous plant cells is now routine, and the selection of the mostappropriate transformation technique will be determined by thepractitioner. The choice of method will vary with the type of plant tobe transformed; those skilled in the art will recognize the suitabilityof particular methods for given plant types. Suitable methods caninclude, but are not limited to: electroporation of plant protoplasts;liposome-mediated transformation; polyethylene glycol (PEG) mediatedtransformation; transformation using viruses; micro-injection of plantcells; micro-projectile bombardment of plant cells; vacuum infiltration;and Agrobacterium tumefaciens mediated transformation. Transformationmeans introducing a nucleotide sequence into a plant in a manner tocause stable or transient expression of the sequence.

Successful examples of the modification of plant characteristics bytransformation with cloned sequences which serve to illustrate thecurrent knowledge in this field of technology, and which are hereinincorporated by reference, include: U.S. Pat. Nos. 5,571,706; 5,677,175;5,510,471; 5,750,386; 5,597,945; 5,589,615; 5,750,871; 5,268,526;5,780,708; 5,538,880; 5,773,269; 5,736,369 and 5,610,042.

Following transformation, plants are preferably selected using adominant selectable marker incorporated into the transformation vector.Typically, such a marker will confer antibiotic or herbicide resistanceon the transformed plants, and selection of transformants can beaccomplished by exposing the plants to appropriate concentrations of theantibiotic or herbicide.

After transformed plants are selected and grown to maturity, thoseplants showing a modified trait are identified. The modified trait canbe any of those traits described above. Additionally, to confirm thatthe modified trait is due to changes in expression levels or activity ofthe polypeptide or polynucleotide of the invention can be determined byanalyzing mRNA expression using Northern blots, RT-PCR or microarrays,or protein expression using immunoblots or Western blots or gel shiftassays.

XVII. INTEGRATED SYSTEMS Sequence Identity

Additionally, the present invention may be an integrated system,computer or computer readable medium that comprises an instruction setfor determining the identity of one or more sequences in a database. Inaddition, the instruction set can be used to generate or identifysequences that meet any specified criteria. Furthermore, the instructionset may be used to associate or link certain functional benefits, suchimproved characteristics, with one or more identified sequence.

For example, the instruction set can include, e.g., a sequencecomparison or other alignment program, e.g., an available program suchas, for example, the Wisconsin Package Version 10.0, such as BLAST,FASTA, PILEUP, FINDPATTERNS or the like (GCG, Madison, Wis.). Publicsequence databases such as GenBank, EMBL, Swiss-Prot and PIR or privatesequence databases such as PHYTOSEQ sequence database (Incyte Genomics,Palo Alto, Calif.) can be searched.

Alignment of sequences for comparison can be conducted by the localhomology algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2:482,by the homology alignment algorithm of Needleman and Wunsch (1970) J.Mol. Biol. 48:443-453, by the search for similarity method of Pearsonand Lipman (1988) Proc. Natl. Acad. Sci. U.S.A. 85:2444-2448, bycomputerized implementations of these algorithms. After alignment,sequence comparisons between two (or more) polynucleotides orpolypeptides are typically performed by comparing sequences of the twosequences over a comparison window to identify and compare local regionsof sequence similarity. The comparison window can be a segment of atleast about 20 contiguous positions, usually about 50 to about 200, moreusually about 100 to about 150 contiguous positions. A description ofthe method is provided in Ausubel et al., supra.

A variety of methods for determining sequence relationships can be used,including manual alignment and computer assisted sequence alignment andanalysis. This later approach is a preferred approach in the presentinvention, due to the increased throughput afforded by computer assistedmethods. As noted above, a variety of computer programs for performingsequence alignment are available, or can be produced by one of skill.

One example algorithm that is suitable for determining percent sequenceidentity and sequence similarity is the BLAST algorithm, which isdescribed in Altschul et al. J. Mol. Biol. 215:403-410 (1990). Softwarefor performing BLAST analyses is publicly available, e.g., through theNational Center for Biotechnology Information (see internet website atncbi.nlm.nih.gov). This algorithm involves first identifying highscoring sequence pairs (HSPs) by identifying short words of length W inthe query sequence, which either match or satisfy some positive-valuedthreshold score T when aligned with a word of the same length in adatabase sequence. T is referred to as the neighborhood word scorethreshold (Altschul et al., supra). These initial neighborhood word hitsact as seeds for initiating searches to find longer HSPs containingthem. The word hits are then extended in both directions along eachsequence for as far as the cumulative alignment score can be increased.Cumulative scores are calculated using, for nucleotide sequences, theparameters M (reward score for a pair of matching residues; always >0)and N (penalty score for mismatching residues; always <0). For aminoacid sequences, a scoring matrix is used to calculate the cumulativescore. Extension of the word hits in each direction are halted when: thecumulative alignment score falls off by the quantity X from its maximumachieved value; the cumulative score goes to zero or below, due to theaccumulation of one or more negative-scoring residue alignments; or theend of either sequence is reached. The BLAST algorithm parameters W, T,and X determine the sensitivity and speed of the alignment. The BLASTNprogram (for nucleotide sequences) uses as defaults a wordlength (W) of11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and acomparison of both strands. For amino acid sequences, the BLASTP programuses as defaults a wordlength (W) of 3, an expectation (E) of 10, andthe BLOSUM62 scoring matrix (see Henikoff & Henikoff (1989) Proc. Natl.Acad. Sci. USA 89:10915). Unless otherwise indicated, “sequenceidentity” here refers to the % sequence identity generated from atblastx using the NCBI version of the algorithm at the default settingsusing gapped alignments with the filter “off” (see, for example,internet website at ncbi.nlm.nih.gov).

In addition to calculating percent sequence identity, the BLASTalgorithm also performs a statistical analysis of the similarity betweentwo sequences (see, e.g., Karlin & Altschul (1993) Proc. Natl. Acad.Sci. USA 90:5873-5787). One measure of similarity provided by the BLASTalgorithm is the smallest sum probability (P(N)), which provides anindication of the probability by which a match between two nucleotide oramino acid sequences would occur by chance. For example, a nucleic acidis considered similar to a reference sequence (and, therefore, in thiscontext, homologous) if the smallest sum probability in a comparison ofthe test nucleic acid to the reference nucleic acid is less than about0.1, or less than about 0.01, and or even less than about 0.001. Anadditional example of a useful sequence alignment algorithm is PILEUP.PILEUP creates a multiple sequence alignment from a group of relatedsequences using progressive, pairwise alignments. The program can align,e.g., up to 300 sequences of a maximum length of 5,000 letters.

The integrated system, or computer typically includes a user inputinterface allowing a user to selectively view one or more sequencerecords corresponding to the one or more character strings, as well asan instruction set which aligns the one or more character strings witheach other or with an additional character string to identify one ormore region of sequence similarity. The system may include a link of oneor more character strings with a particular phenotype or gene function.Typically, the system includes a user readable output element thatdisplays an alignment produced by the alignment instruction set.

The methods of this invention can be implemented in a localized ordistributed computing environment. In a distributed environment, themethods may implemented on a single computer comprising multipleprocessors or on a multiplicity of computers. The computers can belinked, e.g. through a common bus, but more preferably the computer(s)are nodes on a network. The network can be a generalized or a dedicatedlocal or wide-area network and, in certain preferred embodiments, thecomputers may be components of an intra-net or an internet.

Thus, the invention provides methods for identifying a sequence similaror homologous to one or more polynucleotides as noted herein, or one ormore target polypeptides encoded by the polynucleotides, or otherwisenoted herein and may include linking or associating a given plantphenotype or gene function with a sequence. In the methods, a sequencedatabase is provided (locally or across an inter or intra net) and aquery is made against the sequence database using the relevant sequencesherein and associated plant phenotypes or gene functions.

Any sequence herein can be entered into the database, before or afterquerying the database. This provides for both expansion of the databaseand, if done before the querying step, for insertion of controlsequences into the database. The control sequences can be detected bythe query to ensure the general integrity of both the database and thequery. As noted, the query can be performed using a web browser basedinterface. For example, the database can be a centralized publicdatabase such as those noted herein, and the querying can be done from aremote terminal or computer across an internet or intranet.

XVIII. EXAMPLES

The following examples are intended to illustrate but not limit thepresent invention. The complete descriptions of the traits associatedwith each polynucleotide of the invention is fully disclosed in Table 45 and Table 6.

Example I Full Length Gene Identification and Cloning

Putative transcription factor sequences (genomic or ESTs) related toknown transcription factors were identified in the Arabidopsis thalianaGenBank database using the tblastn sequence analysis program usingdefault parameters and a P-value cutoff threshold of −4 or −5 or lower,depending on the length of the query sequence. Putative transcriptionfactor sequence hits were then screened to identify those containingparticular sequence strings. If the sequence hits contained suchsequence strings, the sequences were confirmed as transcription factors.

Alternatively, Arabidopsis thaliana cDNA libraries derived fromdifferent tissues or treatments, or genomic libraries were screened toidentify novel members of a transcription family using a low stringencyhybridization approach. Probes were synthesized using gene specificprimers in a standard PCR reaction (annealing temperature 60° C.) andlabeled with ³²P dCTP using the High Prime DNA Labeling Kit (BoehringerMannheim). Purified radiolabelled probes were added to filters immersedin Church hybridization medium (0.5 M NaPO₄ pH 7.0, 7% SDS, 1% w/vbovine serum albumin) and hybridized overnight at 60° C. with shaking.Filters were washed two times for 45 to 60 minutes with 1×SCC, 1% SDS at60° C.

To identify additional sequence 5′ or 3′ of a partial cDNA sequence in acDNA library, 5′ and 3′ rapid amplification of cDNA ends (RACE) wasperformed using the Marathon™ cDNA amplification kit (Clontech, PaloAlto, Calif.). Generally, the method entailed first isolating poly(A)mRNA, performing first and second strand cDNA synthesis to generatedouble stranded cDNA, blunting cDNA ends, followed by ligation of theMarathon™ Adaptor to the cDNA to form a library of adaptor-ligated dscDNA.

Gene-specific primers were designed to be used along with adaptorspecific primers for both 5′ and 3′ RACE reactions. Nested primers,rather than single primers, were used to increase PCR specificity. Using5′ and 3′ RACE reactions, 5′ and 3′ RACE fragments were obtained,sequenced and cloned. The process can be repeated until 5′ and 3′ endsof the full-length gene were identified. Then the full-length cDNA wasgenerated by PCR using primers specific to 5′ and 3′ ends of the gene byend-to-end PCR.

Example II Construction of Expression Vectors

The sequence was amplified from a genomic or cDNA library using primersspecific to sequences upstream and downstream of the coding region. theexpression vector was pMEN20 or pMEN65, which are both derived frompMON316 (Sanders et al, (1987) Nucleic Acids Research 15:1543-1558) andcontain the caMV 35S promoter to express transgenes. To clone thesequence into the vector, both pmen20 and the amplified DNA fragmentwere digested separately with Sali and Noti restriction enzymes at 37°C. for 2 hours. The digestion products were subject to electrophoresisin a 0.8% agarose gel and visualized by ethidium bromide staining. TheDNA fragments containing the sequence and the linearized plasmid wereexcised and purified by using a Qiaquick gel extraction kit (Qiagen,Valencia Calif.). The fragments of interest were ligated at a ratio of3:1 (vector to insert). Ligation reactions using t4 DNA ligase (NewEngland Biolabs, Beverly, Mass.) were carried out at 16° C. for 16hours. The ligated DNAs were transformed into competent cells of the E.coli strain DH5alpha by using the heat shock method. The transformationswere plated on LB plates containing 50 mg/l kanamycin (Sigma, St. Louis,Mo.). Individual colonies were grown overnight in five milliliters of LBbroth containing 50 mg/l kanamycin at 37° c. Plasmid DNA was purified byusing Qiaquick Mini Prep kits (Qiagen).

Example III Transformation of Agrobacterium with the Expression Vector

After the plasmid vector containing the gene was constructed, the vectorwas used to transform Agrobacterium tumefaciens cells expressing thegene products. The stock of Agrobacterium tumefaciens cells fortransformation were made as described by Nagel et al. (1990) FEMSMicrobiol Letts. 67: 325-328. Agrobacterium strain ABI was grown in 250ml LB medium (Sigma) overnight at 28° C. with shaking until anabsorbance (A₆₀₀) of 0.5-1.0 was reached. Cells were harvested bycentrifugation at 4,000×g for 15 min at 4° C. Cells were thenresuspended in 250 μl chilled buffer (1 mM HEPES, pH adjusted to 7.0with KOH). Cells were centrifuged again as described above andresuspended in 125 μl chilled buffer. Cells were then centrifuged andresuspended two more times in the same HEPES buffer as described aboveat a volume of 100 μl and 750 μl, respectively. Resuspended cells werethen distributed into 40 μl aliquots, quickly frozen in liquid nitrogen,and stored at −80° C.

Agrobacterium cells were transformed with plasmids prepared as describedabove following the protocol described by Nagel et al. For each DNAconstruct to be transformed, 50-100 ng DNA (generally resuspended in 10mM Tris-HCl, 1 mM EDTA, pH 8.0) was mixed with 40 μl of Agrobacteriumcells. The DNA/cell mixture was then transferred to a chilled cuvettewith a 2 mm electrode gap and subject to a 2.5 kV charge dissipated at25 μF and 200 μF using a Gene Pulser II apparatus (Bio-Rad, Hercules,Calif.). After electroporation, cells were immediately resuspended in1.0 ml LB and allowed to recover without antibiotic selection for 2-4hours at 28° C. in a shaking incubator. After recovery, cells wereplated onto selective medium of LB broth containing 100 μg/mlspectinomycin (Sigma) and incubated for 24-48 hours at 28° C. Singlecolonies were then picked and inoculated in fresh medium. The presenceof the plasmid construct was verified by PCR amplification and sequenceanalysis.

Example IV Transformation of Arabidopsis Plants with Agrobacteriumtumefaciens with Expression Vector

After transformation of Agrobacterium tumefaciens with plasmid vectorscontaining the gene, single Agrobacterium colonies were identified,propagated, and used to transform Arabidopsis plants. Briefly, 500 mlcultures of LB medium containing 50 mg/l kanamycin were inoculated withthe colonies and grown at 28° C. with shaking for 2 days until anoptical absorbance at 600 nm wavelength over 1 cm (A₆₀₀) of >2.0 isreached. Cells were then harvested by centrifugation at 4,000×g for 10min, and resuspended in infiltration medium (½×Murashige and Skoog salts(Sigma), 1× Gamborg's B-5 vitamins (Sigma), 5.0% (w/v) sucrose (Sigma),0.044 μM benzylamino purine (Sigma), 200 μl/l Silwet L-77 (Lehle Seeds)until an A₆₀₀ of 0.8 was reached.

Prior to transformation, Arabidopsis thaliana seeds (ecotype Columbia)were sown at a density of ˜10 plants per 4″ pot onto Pro-Mix BX pottingmedium (Hummert International) covered with fiberglass mesh (18 mm×16mm). Plants were grown under continuous illumination (50-75 μE/m²/sec)at 22-23° C. with 65-70% relative humidity. After about 4 weeks, primaryinflorescence stems (bolts) are cut off to encourage growth of multiplesecondary bolts. After flowering of the mature secondary bolts, plantswere prepared for transformation by removal of all siliques and openedflowers.

The pots were then immersed upside down in the mixture of Agrobacteriuminfiltration medium as described above for 30 sec, and placed on theirsides to allow draining into a 1′×2′ flat surface covered with plasticwrap. After 24 h, the plastic wrap was removed and pots are turnedupright. The immersion procedure was repeated one week later, for atotal of two immersions per pot. Seeds were then collected from eachtransformation pot and analyzed following the protocol described below.

Example V Identification of Arabidopsis Primary Transformants

Seeds collected from the transformation pots were sterilized essentiallyas follows. Seeds were dispersed into in a solution containing 0.1%(v/v) Triton X-100 (Sigma) and sterile H₂O and washed by shaking thesuspension for 20 min. The wash solution was then drained and replacedwith fresh wash solution to wash the seeds for 20 min with shaking.After removal of the second wash solution, a solution containing 0.1%(v/v) Triton X-100 and 70% ethanol (Equistar) was added to the seeds andthe suspension was shaken for 5 min. After removal of theethanol/detergent solution, a solution containing 0.1% (v/v) TritonX-100 and 30% (v/v) bleach (Clorox) was added to the seeds, and thesuspension was shaken for 10 min. After removal of the bleach/detergentsolution, seeds were then washed five times in sterile distilled H₂O.The seeds were stored in the last wash water at 4° C. for 2 days in thedark before being plated onto antibiotic selection medium (1× Murashigeand Skoog salts (pH adjusted to 5.7 with 1M KOH), 1× Gamborg's B-5vitamins, 0.9% phytagar (Life Technologies), and 50 mg/l kanamycin).Seeds were germinated under continuous illumination (50-75 μE/m²/sec) at22-23° C. After 7-10 days of growth under these conditions, kanamycinresistant primary transformants (T₁ generation) were visible andobtained. These seedlings were transferred first to fresh selectionplates where the seedlings continued to grow for 3-5 more days, and thento soil (Pro-Mix BX potting medium).

Primary transformants were crossed and progeny seeds (T₂) collected;kanamycin resistant seedlings were selected and analyzed. The expressionlevels of the recombinant polynucleotides in the transformants variesfrom about a 5% expression level increase to a least a 100% expressionlevel increase. Similar observations are made with respect topolypeptide level expression.

Example VI Identification of Arabidopsis Plants with TranscriptionFactor Gene Knockouts

The screening of insertion mutagenized Arabidopsis collections for nullmutants in a known target gene was essentially as described in Krysan etal (1999) Plant Cell 11:2283-2290. Briefly, gene-specific primers,nested by 5-250 base pairs to each other, were designed from the 5′ and3′ regions of a known target gene. Similarly, nested sets of primerswere also created specific to each of the T-DNA or transposon ends (the“right” and “left” borders). All possible combinations of gene specificand T-DNA/transposon primers were used to detect by PCR an insertionevent within or close to the target gene. The amplified DNA fragmentswere then sequenced which allows the precise determination of theT-DNA/transposon insertion point relative to the target gene. Insertionevents within the coding or intervening sequence of the genes weredeconvoluted from a pool comprising a plurality of insertion events to asingle unique mutant plant for functional characterization. The methodis described in more detail in Yu and Adam, U.S. application Ser. No.09/177,733 filed Oct. 23, 1998.

Example VII Identification of Modified Phenotypes in Overexpression orGene Knockout Plants

Experiments were performed to identify those transformants or knockoutsthat exhibited modified biochemical characteristics. Among thebiochemicals that were assayed were insoluble sugars, such as arabinose,fucose, galactose, mannose, rhamnose or xylose or the like; prenyllipids, such as lutein, beta-carotene, xanthophyll-1, xanthophyll-2,chlorophylls A or B, or alpha-, delta- or gamma-tocopherol or the like;fatty acids, such as 16:0 (palmitic acid), 16:1 (palmitoleic acid), 18:0(stearic acid), 18:1 (oleic acid), 18:2 (linoleic acid), 20:0, 18:3(linolenic acid), 20:1 (eicosenoic acid), 20:2, 22:1 (erucic acid) orthe like; waxes, such as by altering the levels of C29, C31, or C33alkanes; sterols, such as brassicasterol, campesterol, stigmasterol,sitosterol or stigmastanol or the like, glucosinolates, protein or oillevels.

Fatty acids were measured using two methods depending on whether thetissue was from leaves or seeds. For leaves, lipids were extracted andesterified with hot methanolic H₂SO₄ and partitioned into hexane frommethanolic brine. For seed fatty acids, seeds were pulverized andextracted in methanol:heptane:toluene:2,2-dimethoxypropane:H₂SO₄(39:34:20:5:2) for 90 minutes at 80° C. After cooling to roomtemperature the upper phase, containing the seed fatty acid esters, wassubjected to GC analysis. Fatty acid esters from both seed and leaftissues were analyzed with a Supelco SP-2330 column.

Glucosinolates were purified from seeds or leaves by first heating thetissue at 95° C. for 10 minutes. Preheated ethanol:water (50:50) is andafter heating at 95° C. for a further 10 minutes, the extraction solventis applied to a DEAE Sephadex column which had been previouslyequilibrated with 0.5 M pyridine acetate. Desulfoglucosinolates wereeluted with 300 ul water and analyzed by reverse phase HPLC monitoringat 226 nm.

For wax alkanes, samples were extracted using an identical method asfatty acids and extracts were analyzed on a HP 5890 GC coupled with a5973 MSD. Samples were chromatographically isolated on a J&W DB35 massspectrometer (J&W Scientific).

To measure prenyl lipids levels, seeds or leaves were pulverized with 1to 2% pyrogallol as an antioxidant. For seeds, extracted samples werefiltered and a portion removed for tocopherol and carotenoid/chlorophyllanalysis by HPLC. The remaining material was saponified for steroldetermination. For leaves, an aliquot was removed and diluted withmethanol and chlorophyll A, chlorophyll B, and total carotenoidsmeasured by spectrophotometry by determining optical absorbance at 665.2nm, 652.5 nm, and 470 nm. An aliquot was removed for tocopherol andcarotenoid/chlorophyll composition by HPLC using a Waters uBondapak C18column (4.6 mm×150 mm). The remaining methanolic solution was saponifiedwith 10% KOH at 80° C. for one hour. The samples were cooled and dilutedwith a mixture of methanol and water. A solution of 2% methylenechloride in hexane was mixed in and the samples were centrifuged. Theaqueous methanol phase was again re-extracted 2% methylene chloride inhexane and, after centrifugation, the two upper phases were combined andevaporated. 2% methylene chloride in hexane was added to the tubes andthe samples were then extracted with one ml of water. The upper phasewas removed, dried, and resuspended in 400 ul of 2% methylene chloridein hexane and analyzed by gas chromatography using a 50 m DB-5 ms (0.25mm ID, 0.25 um phase, J&W Scientific).

Insoluble sugar levels were measured by the method essentially describedby Reiter et al., (1999) Plant Journal 12:335-345. This method analyzesthe neutral sugar composition of cell wall polymers found in Arabidopsisleaves. Soluble sugars were separated from sugar polymers by extractingleaves with hot 70% ethanol. The remaining residue containing theinsoluble polysaccharides was then acid hydrolyzed with allose added asan internal standard. Sugar monomers generated by the hydrolysis werethen reduced to the corresponding alditols by treatment with NaBH₄, thenwere acetylated to generate the volatile alditol acetates which werethen analyzed by GC-FID. Identity of the peaks was determined bycomparing the retention times of known sugars converted to thecorresponding alditol acetates with the retention times of peaks fromwild-type plant extracts. Alditol acetates were analyzed on a SupelcoSP-2330 capillary column (30 m×250 um×0.2 um) using a temperatureprogram beginning at 180° C. for 2 minutes followed by an increase to220° C. in 4 minutes. After holding at 220° C. for 10 minutes, the oventemperature is increased to 240° C. in 2 minutes and held at thistemperature for 10 minutes and brought back to room temperature.

To identify plants with alterations in total seed oil or proteincontent, 150 mg of seeds from T2 progeny plants were subjected toanalysis by Near Infrared Reflectance Spectroscopy (NIRS) using a FossNirSystems Model 6500 with a spinning cup transport system. NIRS is anon-destructive analytical method used to determine seed oil and proteincomposition. Infrared is the region of the electromagnetic spectrumlocated after the visible region in the direction of longer wavelengths.‘Near infrared’ owns its name for being the infrared region near to thevisible region of the electromagnetic spectrum. For practical purposes,near infrared comprises wavelengths between 800 and 2500 nm. NIRS isapplied to organic compounds rich in O—H bonds (such as moisture,carbohydrates, and fats), C—H bonds (such as organic compounds andpetroleum derivatives), and N—H bonds (such as proteins and aminoacids). The NIRS analytical instruments operate by statisticallycorrelating NIRS signals at several wavelengths with the characteristicor property intended to be measured. All biological substances containthousands of C—H, O—H, and N—H bonds. Therefore, the exposure to nearinfrared radiation of a biological sample, such as a seed, results in acomplex spectrum which contains qualitative and quantitative informationabout the physical and chemical composition of that sample.

The numerical value of a specific analyte in the sample, such as proteincontent or oil content, is mediated by a calibration approach known aschemometrics. Chemometrics applies statistical methods such as multiplelinear regression (MLR), partial least squares (PLS), and principlecomponent analysis (PCA) to the spectral data and correlates them with aphysical property or other factor, that property or factor is directlydetermined rather than the analyte concentration itself. The methodfirst provides “wet chemistry” data of the samples required to developthe calibration.

Calibration for Arabidopsis seed oil composition was performed usingaccelerated solvent extraction using 1 g seed sample size and wasvalidated against certified canola seed. A similar wet chemistryapproach was performed for seed protein composition calibration.

Data obtained from NIRS analysis was analyzed statistically using anearest-neighbor (N—N) analysis. The N—N analysis allows removal ofwithin-block spatial variability in a fairly flexible fashion which doesnot require prior knowledge of the pattern of variability in thechamber. Ideally, all hybrids are grown under identical experimentalconditions within a block (rep). In reality, even in many block designs,significant within-block variability exists. Nearest-neighbor proceduresare based on assumption that environmental effect of a plot is closelyrelated to that of its neighbors. Nearest-neighbor methods useinformation from adjacent plots to adjust for within-block heterogeneityand so provide more precise estimates of treatment means anddifferences. If there is within-plot heterogeneity on a spatial scalethat is larger than a single plot and smaller than the entire block,then yields from adjacent plots will be positively correlated.Information from neighboring plots can be used to reduce or remove theunwanted effect of the spatial heterogeneity, and hence improve theestimate of the treatment effect. Data from neighboring plots can alsobe used to reduce the influence of competition between adjacent plots.The Papadakis N—N analysis can be used with designs to removewithin-block variability that would not be removed with the standardsplit plot analysis (Papadakis, 1973, Inst. d'Amelior. PlantesThessaloniki (Greece) Bull. Scientif., No. 23; Papadakis, 1984, Proc.Acad. Athens, 59, 326-342).

Experiments were performed to identify those transformants or knockoutsthat exhibited an improved pathogen tolerance. For such studies, thetransformants were exposed to biotropic fungal pathogens, such asErysiphe orontii, and necrotropic fungal pathogens, such as Fusariumoxysporum. Fusarium oxysporum isolates cause vascular wilts and dampingoff of various annual vegetables, perennials and weeds (Mauch-Mani andSlusarenko (1994) Molecular Plant-Microbe Interactions 7: 378-383). ForFusarium oxysporum experiments, plants grown on Petri dishes weresprayed with a fresh spore suspension of F. oxysporum. The sporesuspension was prepared as follows: A plug of fungal hyphae from a plateculture was placed on a fresh potato dextrose agar plate and allowed tospread for one week. 5 ml sterile water was then added to the plate,swirled, and pipetted into 50 ml Armstrong Fusarium medium. Spores weregrown overnight in Fusarium medium and then sprayed onto plants using aPreval paint sprayer. Plant tissue was harvested and frozen in liquidnitrogen 48 hours post infection.

Erysiphe orontii is a causal agent of powdery mildew. For Erysipheorontii experiments, plants were grown approximately 4 weeks in agreenhouse under 12 hour light (20° C., ˜30% relative humidity (rh)).Individual leaves were infected with E. orontii spores from infectedplants using a camel's hair brush, and the plants were transferred to aPercival growth chamber (20° C., 80% rh.). Plant tissue was harvestedand frozen in liquid nitrogen 7 days post infection.

Botrytis cinerea is a necrotrophic pathogen. Botrytis cinerea was grownon potato dextrose agar in the light. A spore culture was made byspreading 10 ml of sterile water on the fungus plate, swirling andtransferring spores to 10 ml of sterile water. The spore inoculum(approx. 105 spores/ml) was used to spray 10 day-old seedlings grownunder sterile conditions on MS (minus sucrose) media. Symptoms wereevaluated every day up to approximately 1 week.

Infection with bacterial pathogens Pseudomonas syringae pv maculicola(Psm) strain 4326 and pv maculicola strain 4326 was performed by handinoculation at two doses. Two inoculation doses allows thedifferentiation between plants with enhanced susceptibility and plantswith enhanced resistance to the pathogen. Plants were grown for 3 weeksin the greenhouse, then transferred to the growth chamber for theremainder of their growth. Psm ES4326 was hand inoculated with 1 mlsyringe on 3 fully-expanded leaves per plant (4½ wk old), using at least9 plants per overexpressing line at two inoculation doses, OD=0.005 andOD=0.0005. Disease scoring occurred at day 3 post-inoculation withpictures of the plants and leaves taken in parallel.

In some instances, expression patterns of the pathogen-induced genes(such as defense genes) was monitored by microarray experiments. cDNAswere generated by PCR and resuspended at a final concentration of ˜100ng/ul in 3×SSC or 150 mM Na-phosphate (Eisen and Brown (1999) MethodsEnzymol. 303:179-205). The cDNAs were spotted on microscope glass slidescoated with polylysine. The prepared cDNAs were aliquoted into 384 wellplates and spotted on the slides using an x-y-z gantry (OmniGrid)purchased from GeneMachines (Menlo Park, Calif.) outfitted with quilltype pins purchased from Telechem International (Sunnyvale, Calif.).After spotting, the arrays were cured for a minimum of one week at roomtemperature, rehydrated and blocked following the protocol recommendedby Eisen and Brown (1999; supra).

Sample total RNA (10 ug) samples were labeled using fluorescent Cy3 andCy5 dyes. Labeled samples were resuspended in 4×SSC/0.03% SDS/4 ugsalmon sperm DNA/2 ug tRNA/50 mM Na-pyrophosphate, heated for 95° C. for2.5 minutes, spun down and placed on the array. The array was thencovered with a glass coverslip and placed in a sealed chamber. Thechamber was then kept in a water bath at 62° C. overnight. The arrayswere washed as described in Eisen and Brown (1999) and scanned on aGeneral Scanning 3000 laser scanner. The resulting files aresubsequently quantified using Imagene, a software purchased fromBioDiscovery (Los Angeles, Calif.).

Experiments were performed to identify those transformants or knockoutsthat exhibited an improved environmental stress tolerance. For suchstudies, the transformants were exposed to a variety of environmentalstresses. Plants were exposed to chilling stress (6 hour exposure to4-8° C.), heat stress (6 hour exposure to 32-37° C.), high salt stress(6 hour exposure to 200 mM NaCl), drought stress (168 hours afterremoving water from trays), osmotic stress (6 hour exposure to 3 Mmannitol), or nutrient limitation (nitrogen, phosphate, and potassium)(Nitrogen: all components of MS medium remained constant except N wasreduced to 20 mg/l of NH₄NO₃, or Phosphate: All components of MS mediumexcept KH₂PO₄, which was replaced by K₂SO₄, Potassium: All components ofMS medium except removal of KNO₃ and KH₂PO₄, which were replaced byNaH₄PO₄).

Experiments were performed to identify those transformants or knockoutsthat exhibited a modified structure and development characteristics. Forsuch studies, the transformants were observed by eye to identify novelstructural or developmental characteristics associated with the ectopicexpression of the polynucleotides or polypeptides of the invention.

Experiments were performed to identify those transformants or knockoutsthat exhibited modified sugar-sensing. For such studies, seeds fromtransformants were germinated on media containing 5% glucose or 9.4%sucrose which normally partially restrict hypocotyl elongation. Plantswith altered sugar sensing may have either longer or shorter hypocotylsthan normal plants when grown on this media. Additionally, other planttraits may be varied such as root mass.

Flowering time was measured by the number of rosette leaves present whena visible inflorescence of approximately 3 cm is apparent Rosette andtotal leaf number on the progeny stem are tightly correlated with thetiming of flowering (Koomneef et al (1991) Mol. Gen. Genet. 229:57-66.The vernalization response was measured. For vernalization treatments,seeds were sown to MS agar plates, sealed with micropore tape, andplaced in a 4° C. cold room with low light levels for 6-8 weeks. Theplates were then transferred to the growth rooms alongside platescontaining freshly sown non-vernalized controls. Rosette leaves werecounted when a visible inflorescence of approximately 3 cm was apparent.

Modified phenotypes observed for particular overexpressor or knockoutplants are provided in Table 5. For a particular overexpressor thatshows a less beneficial characteristic, it may be more useful to selecta plant with a decreased expression of the particular transcriptionfactor. For a particular knockout that shows a less beneficialcharacteristic, it may be more useful to select a plant with anincreased expression of the particular transcription factor.

The sequences of the Sequence Listing or those in Tables 4, Table 5 orthose disclosed here can be used to prepare transgenic plants and plantswith altered traits. The specific transgenic plants listed below areproduced from the sequences of the Sequence Listing, as noted. Table 5provides exemplary polynucleotide and polypeptide sequences of theinvention. Table 5 includes, from left to right for each sequence: thefirst column shows the polynucleotide SEQ ID NO; the second column showsthe Mendel Gene ID No., GID; the third column shows the trait(s)resulting from the knock out or overexpression of the polynucleotide inthe transgenic plant; the fourth column shows the category of the trait;the fifth column shows the transcription factor family to which thepolynucleotide belongs; the sixth column (“Comment”), includes specificeffects and utilities conferred by the polynucleotide of the firstcolumn; the seventh column shows the SEQ ID NO of the polypeptideencoded by the polynucleotide; and the eighth column shows the aminoacid residue positions of the conserved domain in amino acid (AA)co-ordinates.

Seed of plants overexpressing sequences G265 (SEQ ID NOs:871 and 872),G715 (SEQ ID NOs:925 and 926), G1471 (SEQ ID NOs:311 and 312), G1793(SEQ ID NOs:365 and 366), G1838 (SEQ ID NOs:381 and 382), G1902 (SEQ IDNOs:405 and 406), G286 (SEQ ID NOs:877 and 878), G2138 (SEQ ID NOs:865and 866) and G2830 (SEQ ID NOs:875 and 876) was subjected to NIRanalysis and a significant increase in seed oil content compared withseed from control plants was identified.

G192: G192 (SEQ ID NO: 859) was expressed in all plant tissues and underall conditions examined. Its expression was slightly induced uponinfection by Fusarium. G192 was analyzed using transgenic plants inwhich this gene was expressed under the control of the 35S promoter.G192 overexpressors were late flowering under 12 hour light and had moreleaves than control plants. This phenotype was manifested in the threeT2 lines analyzed. Results of one experiment suggest that G192overexpressor was more susceptible to infection with a moderate dose ofthe fungal pathogen Erysiphe orontii. The decrease in seed oil observedfor one line was replicated in an independent experiment. G192overexpression delayed flowering. A wide variety of applications existfor systems that either lengthen or shorten the time to flowering, orfor systems of inducible flowering time control. In particular, inspecies where the vegetative parts of the plants constitute the crop andthe reproductive tissues are discarded, it will be advantageous to delayor prevent flowering. Extending vegetative development can bring aboutlarge increases in yields. G192 can be used to manipulate the defenseresponse in order to generate pathogen-resistant plants. G192 can beused to manipulate seed oil content, which can be of nutritional value.

Closely Related Genes from Other Species

G192 had some similarity within the conserved WRKY domain tonon-Arabidopsis plant proteins.

G1946: G1946 (SEQ ID NO: 801) was studied using transgenic plants inwhich the gene was expressed under the control of the 35S promoter.Overexpression of G1946 resulted in accelerated flowering, with35S::G1946 transformants producing flower buds up to a week earlier thanwild-type controls (24-hour light conditions). These effects were seenin 12/20 primary transformants and in two independent plantings of eachof the three T2 lines. Unlike many early flowering Arabidopsistransgenic lines, which are dwarfed, 35S::G1946 transformants oftenreached full-size at maturity, and produced large quantities of seeds,although the plants were slightly pale in coloration and had slightlyflat leaves compared to wild-type. In addition, 35S::G1946 plants showedan altered response to phosphate deprivation. Seedlings of G1946overexpressor plants showed more secondary root growth on phosphate-freemedia, when compared to wild-type control. In a repeat experiment, allthree lines showed the phenotype. Overexpression of G1946 in Arabidopsisalso resulted in an increase in seed glucosinolate M39501 in T2 linesland 3. An increase in seed oil and a decrease in seed protein was alsoobserved in these two lines. G1946 was ubiquitously expressed, and doesnot appear to be significantly induced or repressed by any of the bioticand abiotic stress conditions tested at this time, with the exception ofcold, which repressed G1946 expression. G1946 can be used to modifyflowering time, as well as to improve the plant's performance inconditions of limited phosphate, and to alter seed oil, protein, andglucosinolate composition.

Closely Related Genes from Other Species

A comparison of the amino acid sequence of G1946 with sequencesavailable from GenBank showed strong similarity with plant HSFs ofseveral species (Lycopersicon peruvianum, Medicago truncatula,Lycopersicon esculentum, Glycine max, Solanum tuberosum, Oryza sativaand Hordeum vulgare subsp. vulgare).

G375: The sequence of G375 (SEQ ID NO:239) was experimentally determinedand G375 was analyzed using transgenic plants in which G375 wasexpressed under the control of the 35S promoter. Overexpression of G375produced marked effects on leaf development. At early stages of growth,35S::G375 seedlings developed narrow, upward pointing leaves with longpetioles (possibly indicating a disruption in circadian-clock controlledprocesses or nyctinastic movements). Additionally, some seedlings werenoted to have elongated hypocotyls, and some were rather small comparedto wild-type controls. Comparable phenotypes were obtained byoverexpression of an AP2 family gene, G2113 (SEQ ID NO: 85). Followingthe switch to flowering, 35S::G375 plants showed reduced fertility,which possibly arose from a failure of stamens to fully elongate. One ofthe three T2 lines, (#41) was later flowering than wild-type controls,and also developed large numbers of small secondary rosette leaves inthe axils of the primary rosette. Although these effects were not notedin the other two lines, the phenotypes obtained in line 41 were somewhatsimilar to those produced by overexpression of another Z-dof gene, G736(SEQ ID NO: 211). G375 was expressed in all tissues, although atdifferent levels. It was expressed at low levels in the root andgerminating seed, and expressed at high levels in the embryo. Theeffects of G375 on leaf architecture are of potential interest to theornamental horticulture industry.

Closely Related Genes from Other Species

G375 showed some homology to non-Arabidopsis plant proteins within theconserved D of domain.

G1255: The sequence of G1255 (SEQ ID NO: 273) was experimentallydetermined and G1255 was analyzed using transgenic plants in which G1255was expressed under the control of the 35S promoter. Plantsoverexpressing G1255 had alterations in leaf architecture, a reductionin apical dominance, an increase in seed size, and showed more diseasesymptoms following inoculation with a low dose of the fungal pathogenBotrytis cinerea. G1255 was constitutively expressed and notsignificantly induced by any conditions tested. On the basis of thephenotypes produced by overexpression of G1255, G1255 can be used tomanipulate the plant's defense response to produce pathogen resistance,alter plant architecture, or alter seed size.

Closely Related Genes from Other Species

G1255 showed strong homology to a putative rice zing finger proteinrepresented by sequence AC087181_(—)3. Sequence identity between thesetwo protein extended beyond the conserved domain, and therefore, thesegenes can be orthologs.

G865: The complete cDNA sequence of G865 (SEQ ID NO: 557) wasdetermined. G865 was ubiquitously expressed in Arabidopsis tissues. G865was analyzed using transgenic plants in which G865 was expressed underthe control of the 35S promoter. Plants overexpressing G865 were earlyflowering, with numerous secondary inflorescence meristems giving them abushy appearance. G865 overexpressors were more susceptible to infectionwith a moderate dose of the fungal pathogens Erysiphe orontii andBotrytis cinerea. In addition, seeds from G865 overexpressing plantsshowed a trend of increased protein and reduced oil content, althoughthe observed changes were not beyond the criteria used for judgingsignificance except in one line. G865 can be used to control floweringtime. G865 can be used to manipulate the defense response in order togenerate pathogen-resistant plants. G865 can be used to alter seed oiland protein content of a plant.

Closely Related Genes from Other Species

G865 and other non-Arabidopsis AP2/EREBP proteins were similar withinthe conserved AP2 domain.

G2509: G2509 (SEQ ID NO: 23) was studied using transgenic plants inwhich the gene was expressed under the control of the 35S promoter.Overexpression of G2509 caused multiple alterations in plant growth anddevelopment, most notably, altered branching patterns, and a reductionin apical dominance, giving the plants a shorter, more bushy staturethan wild type. Twenty 35S::G2509 primary transformants were examined;at early stages of rosette development, these plants displayed awild-type phenotype. However, at the switch to flowering, almost all T1lines showed a marked loss of apical dominance and large numbers ofsecondary shoots developed from axils of primary rosette leaves. In themost extreme cases, the shoots had very short internodes, giving theinflorescence a very bushy appearance. Such shoots were often very thinand flowers were relatively small and poorly fertile. At later stages,many plants appeared very small and had a low seed yield compared towild type. In addition to the effects on branching, a substantial numberof 35S::G2509 primary transformants also flowered early and had budsvisible several days prior to wild type. Similar effects oninflorescence development were noted in each of three T2 populationsexamined. The branching and plant architecture phenotypes observed in35S::G2509 lines resemble phenotypes observed for three other AP2/EREBPgenes: G865 (SEQ ID NO: 557), G1411 (SEQ ID NO: 3), and G1794 (SEQ IDNO: 13). G2509, G865, and G1411 form a small clade within the largeAP2/EREBP family, and G1794, although not belonging to the clade, is oneof the AP2/EREBP genes closest to it in the phylogenetic tree. It isthus likely that all these genes share a related function, such asaffecting hormone balance. Overexpression of G2509 in Arabidopsisresulted in an increase in alpha-tocopherol in seeds in T2 lines 5 and11. G2509 was ubiquitously expressed in Arabidopsis plant tissue. G2509expression levels were altered by a variety of environmental orphysiological conditions. G2509 can be used to manipulate plantarchitecture and development. G2509 can be used to alter tocopherolcomposition. Tocopherols have anti-oxidant and vitamin E activity. G2509can be useful in altering flowering time. A wide variety of applicationsexist for systems that either lengthen or shorten the time to flowering.

Closely Related Genes from Other Species

G2509 showed some sequence similarity with known genes from other plantspecies within the conserved AP2/EREBP domain.

G2347: G2347 (SEQ ID NO: 1119) was analyzed using transgenic plants inwhich G2347 was expressed under the control of the 35S promoter.Overexpression of G2347 markedly reduced the time to flowering inArabidopsis. This phenotype was apparent in the majority of primarytransformants and in all plants from two out of the three T2 linesexamined. Under continuous light conditions, 35S::G2347 plants formedflower buds up a week earlier than wild type. Many of the plants wererather small and spindly compared to controls. To demonstrate thatoverexpression of G2347 could induce flowering under less inductivephotoperiods, two T2 lines were re-grown in 12 hour conditions; again,all plants from both lines bolted early, with some initiating flowerbuds up to two weeks sooner than wild-type. As determined by RT-PCR,G2347 was highly expressed in rosette leaves and flowers, and to muchlower levels in embryos and siliques. No expression of G2347 wasdetected in the other tissues tested. G2347 expression was repressed bycold, and by auxin treatments and by infection by Erysiphe. G2347 isalso highly similar to the Arabidopsis protein G2010 (SEQ ID NO: 1121).The level of homology between these two proteins suggested they couldhave similar, overlapping, or redundant functions in Arabidopsis. Insupport of this hypothesis, overexpression of both G2010 and G2347resulted in early flowering phenotypes in transgenic plants.

Closely Related Genes from Other Species

The closest relative to G2347 is the Antirrhinum protein, SBP2(CAA63061). The similarity between these two proteins is extensiveenough to suggest they might have similar functions in a plant.

G988: G988 (SEQ ID NO: 43) was analyzed using transgenic plants in whichG988 was expressed under the control of the 35S promoter. Plantsoverexpressing G988 had multiple morphological phenotypes. Thetransgenic plants were generally smaller than wild-type plants, hadaltered leaf, inflorescence and flower development, altered plantarchitecture, and altered vasculature. In one transgenic lineoverexpressing G988 (line 23), an increase in the seed glucosinolateM39489 was observed. The phenotype of plants overexpressing G988 waswild-type in all other assays performed. In wild-type plants, G988 wasexpressed primarily in flower and silique tissue, but was also presentat detectable levels in all other tissues tested. Expression of G988 wasinduced in response to heat treatment, and repressed in response toinfection with Erysiphe. Based on the observed morphological phenotypesof the transgenic plants, G988 can be used to create plants with largerflowers. This can have value in the ornamental horticulture industry.The reduction in the formation of lateral branches suggests that G988can have utility on the forestry industry. The Arabidopsis plantsoverexpressing G988 also had reduced fertility. This could actually be adesirable trait in some instances, as it can be exploited to prevent orminimize the escape of GMO (genetically modified organism) pollen intothe environment.

Closely Related Genes from Other Species

The amino acid sequence for the Capsella rubella hypothetical proteinrepresented by GenBank accession number CRU303349 was significantlyidentical to G988 outside of the SCR conserved domains. The Capsellarubella hypothetical protein is 90% identical to G988 over a stretch ofroughly 450 amino acids. Therefore, it is likely that the Capsellarubella gene is an ortholog of G988.

G2346: G2346 (SEQ ID NO: 459) was analyzed using transgenic plants inwhich the gene was expressed under the control of the 35S promoter.35S::G2346 seedlings from all three T2 populations had slightly largercotyledons and appeared somewhat more advanced than controls. Thisindicated that the seedlings developed more rapidly that the controlplants. At later stages, however, G2346 overexpressing plants showed noconsistent differences from control plants. The phenotype of thesetransgenic plants was wild-type in all other assays performed. Accordingto RT-PCR analysis, G2346 is expressed ubiquitously.

Closely Related Genes from Other Species

G2346 shows some sequence similarity with known genes from other plantspecies within the conserved SBP domain.

G1354: The complete sequence of G1354 (SEQ ID NO: 285) was determined.G1354 was analyzed using transgenic plants in which G1354 was expressedunder the control of the 35S promoter. Overexpression of G1354 producedhighly deleterious effects on growth and development. Only three35S::G1354 T1 plants were obtained; all were extremely tiny and slowdeveloping. After three weeks of growth, each of the plants comprised acompletely disorganized mass of leaves and root that had no clear axisof growth. Since these individuals would not have survivedtransplantation to soil, they were harvested for RT-PCR analysis; allthree plants showed moderate levels of G1354 overexpression compared towhole wild-type seedlings of an equivalent size. Only a very smallnumber of transformants were obtained from two selection attempts onseparate batches of T0 seed. Usually between 15 and 120 transformantsare obtained from each aliquot of 300 mg T0 seed from wild-type plants.The low transformation frequency obtained in this experiment suggeststhat high levels of G1354 overexpression might have completely lethaleffects and prevent transformed seeds from germinating. As determined byRT-PCR, G1354 was uniformly expressed in all tissues and under allconditions tested in RT-PCR. However, the gene was repressed in leaftissue in response to Erysiphe infection.

Closely Related Genes from Other Species

G1354 is closely related to a NAM protein encoded by polynucleotide fromrice (AC005310). Similarity between G1354 and this rice protein extendsbeyond the signature motif of the family to a level that would suggestthe genes are orthologs.

G1063: G1063 (SEQ ID NO: 119) is a member of a clade of highly relatedHLH/MYC proteins that also includes G779 (SEQ ID NO: 113), G1499 (SEQ IDNO: 7), G2143 (SEQ ID NO: 129), and G2557 (SEQ ID NO: 133). All of thesegenes caused similar pleiotropic phenotypic effects when overexpressed,the most striking of which was the production of ectopic carpelloidtissue. These genes can be considered key regulators of carpeldevelopment. A spectrum of developmental alterations was observedamongst 35S::G1063 primary transformants and the majority were markedlysmall, dark green, and had narrow curled leaves. The most severelyaffected individuals were completely sterile and formed highly abnormalinflorescences; shoots often terminated in pin-like structures, andflowers were replaced by filamentous carpelloid structures. In othercases, flowers showed internode elongation between floral whorls, with acentral carpel protruding on a pedicel-like organ. Additionally, lateralbranches sometimes failed to develop and tiny patches of carpelloidtissue formed at axillary nodes of the inflorescence. In lines with anintermediate phenotype, flowers contained defined whorls of organs, butsepals were converted to carpelloid structures or displayed patches ofcarpelloid tissue. In contrast, lines with a weak phenotype developedrelatively normal flowers and produced a reasonable quantity of seed.Such plants were still distinctly smaller than wild-type controls. Sincethe strongest 35S::G1063 lines were sterile, three lines with arelatively weak phenotype, that had produced sufficient seed forbiochemical and physiological analysis, were selected for further study.Two of the T2 populations (T2-28,37) were clearly small, darker greenand possessed narrow leaves compared to wild type. Plants from one ofthese populations (T2-28) also produced occasional branches withabnormal flowers like those seen in the T1. The final T2 population(T2-30) displayed a very mild phenotype. Overexpression of G1063 inArabidopsis resulted in a decrease in seed oil content in T2 lines 28and 37. No altered phenotypes were detected in any of the physiologicalassays, except that the plants were noted to be somewhat small andproduce anthocyanin when grown in Petri plates. G1063 was expressed atlow to moderate levels in roots, flowers, rosette leaves, embryos, andgerminating seeds, but was not detected in shoots or siliques. It wasinduced by auxin. G1063 can be used to manipulate flower form andstructure or plant fertility. One application for manipulation of flowerstructure can be in the production of saffron, which is derived from thestigmas of Crocus sativus. G1063 has utility in manipulating seed oiland protein content.

Closely Related Genes from Other Species

G1063 protein shared extensive homology in the basic helix loop helixregion with a protein sequence encoded by Glycine max cDNA clone(AW832545) as well as a tomato root, plants pre-anthesis Lycopersiconsculentum cDNA (BE451174).

G2143: G2143 (SEQ ID NO: 129) is a member of a clade of highly relatedHLH/MYC proteins that also includes G779 (SEQ ID NO: 113), G1063 (SEQ IDNO: 119), G1499 (SEQ ID NO: 7), and G2557 (SEQ ID NO: 133). All of thesegenes caused similar pleiotropic phenotypic effects when overexpressed,the most striking of which was the production of ectopic carpelloidtissue. These genes can be considered key regulators of carpeldevelopment. Twelve out of twenty 35S::G2143 T1 lines showed a verysevere phenotype; these plants were markedly small and had narrow,curled, dark-green leaves. Such individuals were completely sterile andformed highly abnormal inflorescences; shoots often terminated inpin-like structures, and flowers were replaced by filamentous carpelloidstructures, or a fused mass of carpelloid tissue. Furthermore, lateralbranches usually failed to develop, and tiny patches of stigmatic tissueoften formed at axillary nodes of the inflorescence. Strongly affectedplants displayed the highest levels of transgene expression (determinedby RT-PCR). The remaining T1 lines showed lower levels of G2143overexpression; these plants were still distinctly smaller than wildtype, but had relatively normal inflorescences and produced seed. Sincethe strongest 35S::G2143 lines were sterile, three lines with arelatively weak phenotype, that had produced sufficient seed forbiochemical analysis, were selected for further study. T2-11 plantsdisplayed a very mild phenotype and had somewhat small, narrow, darkgreen leaves. The other two T2 populations, however, appeared wild-type,suggesting that transgene activity might have been reduced between thegenerations. Reduced seedling vigor was noted in the physiologicalassays. G2143 expression was detected at low levels in flowers andsiliques, and at higher levels in germinating seed. G2143 can be used tomanipulate flower form and structure or plant fertility. One applicationfor manipulation of flower structure can be in the production ofsaffron, which is derived from the stigmas of Crocus sativus.

Closely Related Genes from Other Species

G2143 protein shared extensive homology in the basic helix loop helixregion with a protein encoded by Glycine max cDNA clones (AW832545,BG726819 and BG154493) and a Lycopersicon esculentum cDNA clone(BE451174). There was lower homology outside of the region.

G2557: G2557 (SEQ ID NO: 133) is a member of a clade of highly relatedHLH/MYC proteins that also includes G779 (SEQ ID NO: 113), G1063 (SEQ IDNO: 119), G1499 (SEQ ID NO: 7), and G2143 (SEQ ID NO: 129). All of thesegenes caused similar pleiotropic phenotypic effects when overexpressed,the most striking of which was the production of ectopic carpelloidtissue. These genes can be considered key regulators of carpeldevelopment. The flowers of 35S::G2557 primary transformants displayedpatches of stigmatic papillae on the sepals, and often had rather narrowpetals and poorly developed stamens. Additionally, carpels were alsooccasionally held outside of the flower at the end of an elongatedpedicel like structure. As a result of such defects, 35S::G2557 plantsoften showed very poor fertility and formed small wrinkled siliques. Inaddition to such floral abnormalities, the majority of primarytransformants were also small and darker green in coloration than wildtype. Approximately one third of the T1 plants were extremely tiny andcompletely sterile. Three T1 lines (#7,9,12), that had produced someseeds, and showed a relatively weak phenotype, were chosen for furtherstudy. All three of the T2 populations from these lines contained plantsthat were distinctly small, had abnormal flowers, and were poorlyfertile compared to controls. Stigmatic tissue was not noted on thesepals of plants from these three T2 lines. Another line (#4) that hadshown a moderately strong phenotype in the T1 was sown for onlymorphological analysis in the T2 generation. T2-4 plants were small,dark green, and produced abnormal flowers with ectopic stigmatic tissueon the sepals, as had been seen in the parental plant. G2557 expressionwas detected at low to moderate levels in all tissues tested exceptshoots. It was induced by cold, heat, and salt, and repressed bypathogen infection. G1063 can be used to manipulate flower form andstructure or plant fertility. One application for manipulation of flowerstructure can be in the production of saffron, which is derived from thestigmas of Crocus sativus.

Closely Related Genes from Other Species

G2557 protein shows extensive sequence similarity in the region of basichelix loop helix with a protein encoded by Glycine max cDNA clone(BE347811).

G2430: The complete sequence of G2430 (SEQ ID NO: 697) was determined.G2430 is a member of the response regulator class of GARP proteins (ARRgenes), although one of the two conserved aspartate residuescharacteristic of response regulators is not present. The secondaspartate, the putative phosphorylated site, is retained so G2430 canhave response regulator function. G2430 is specifically expressed inembryo and silique tissue. In morphological analyses, plantsoverexpressing G2430 showed more rapid growth than control plants atearly stages, and in two of three lines examined produced large, flatleaves. Early flowering was observed for some lines, but this effect wasinconsistent between plantings. G2430 can regulate plant growth.Overexpression of G2430 in Arabidopsis also resulted in seedlings thatare slightly more tolerant to heat in a germination assay. Seedlingsfrom G2430 overexpressing transgenic plants were slightly greener thanthe control seedlings under high temperature conditions. In a repeatexperiment on individual lines, G2430 line 15 showed the strongest heattolerant phenotype. G2430 can be useful to promote faster developmentand reproduction in plants.

Closely Related Genes from Other Species

G2430 had some similarity within of the conserved GARP andresponse-regulator domains to non-Arabidopsis proteins.

G1478: The sequence of G1478 (SEQ ID NO: 831) was determined and G1478was analyzed using transgenic plants in which G1478 was expressed underthe control of the 35S promoter. Plants overexpressing G1478 had ageneral delay in progression through the life cycle, in particular adelay in flowering time. G1478 is expressed at higher levels in flowers,rosettes and embryos but otherwise expression is constitutive. Based onthe phenotypes produced through G1478 overexpression, G1478 can be usedto manipulate the rate at which plants grow, and flowering time.

Closely Related Genes from Other Species

G1478 shows some homology to non-Arabidopsis proteins within theconserved domain.

G681: G681 (SEQ ID NO: 579) was analyzed using transgenic plants inwhich the gene was expressed under the control of the 35S promoter.Approximately half of the 35S::G681 primary transformants were markedlysmall and formed narrow leaves compared to controls. These plants oftenproduced thin inflorescence stems, had rather poorly formed flowers withlow pollen production, and set few seeds. Three T1 lines with relativelyweak phenotypes, which had produced reasonable quantities of seed, wereselected for further study. Plants from one of the T2 populations werenoted to be slightly small, but otherwise the T2 lines displayed noconsistent differences in morphology from controls. In leaves of two ofthe T2 lines, overexpression of G681 resulted in an increase in thepercentage of the glucosinolate M39480. According to RT-PCR analysis,G681 expression was detected at very low levels in flower and rosetteleaf tissues. G681 was induced by drought stress. G681 can be used toalter glucosinolate composition in plants. Increases or decreases inspecific glucosinolates or total glucosinolate content are desirabledepending upon the particular application. For example: (1)Glucosinolates are undesirable components of the oilseeds used in animalfeed, since they produce toxic effects. Low-glucosinolate varieties ofcanola have been developed to combat this problem. (2) Someglucosinolates have anti-cancer activity; thus, increasing the levels orcomposition of these compounds might be of interest from a nutraceuticalstandpoint. (3) Glucosinolates form part of a plants natural defenseagainst insects. Modification of glucosinolate composition or quantitycould therefore afford increased protection from predators. Furthermore,in edible crops, tissue specific promoters can be used to ensure thatthese compounds accumulate specifically in tissues, such as theepidermis, which are not taken for consumption.

Closely Related Genes from Other Species

G681 shows some sequence similarity with known genes from other plantspecies within the conserved Myb domain.

G878: G878 (SEQ ID NO: 611) was studied using transgenic plants in whichthe gene was expressed under the control of the 35S promoter. Analysisof primary transformants revealed that overexpression of G878 delays theonset of flowering in Arabidopsis. 11/20 of the 35S::G878 T1 plantsflowered approximately one week later than wild type under continuouslight conditions. These plants were also darker green, had shorterstems, and senesced later than controls. G878 was ubiquitouslyexpressed. G878 can be used to modify flowering time and senescence, anda wide variety of applications exist for systems that either lengthen orshorten the time to flowering.

Closely Related Genes from Other Species

G878 was highly related to other WRKY proteins from a variety of plantspecies, such as the Nicotiana tabacum DNA-binding protein 2 (WRKY2)(AF096299), and a Cucumis sativus SPF1-like DNA-binding protein(L44134).

G374: G374 (SEQ ID NO: 47) was expressed at low levels throughout theplant and was induced by salicylic acid. G374 was investigated usinglines carrying a T-DNA insertion in this gene. The T-DNA insertion wasapproximately three quarters of the way into the protein coding sequenceand should result in a null mutation. Homozygosity for a T-DNA insertionwithin G374 caused lethality at early stages of embryo development. Inan initial screen for G374 knockouts, heterozygous plants wereidentified. Seed from those individuals was sown to soil and elevenplants were PCR-screened to identify homozygotes. No homozygotes wereobtained; 6 of the progeny were heterozygous whilst the other 5 werewild type. This raised the prospect that homozygosity for the G374insertion was lethal. To examine this possibility further, heterozygousKO.G374 plants were re-grown. These individuals looked wild type, buttheir siliques were examined for seed abnormalities. When green siliqueswere dissected, around 25% of developing seeds were white or aborted.Embryos from these siliques were cleared using Hoyers solution, andexamined under the microscope. It was apparent that embryos from thewhite seeds had arrested at early (globular or heart) stages ofdevelopment, whilst embryos from the normal seeds were fully developed.Such arrested or aborted seeds most likely represented homozygotes forthe G374 insertion. To support this conclusion, seed was collected fromheterozygous plants and sown to kanamycin plates (the T-DNA insertioncarried the NPT marker gene). Of the seedlings that germinated, 160 werekanamycin resistant and 107 were kanamycin sensitive. These data moreclosely fitted a 2:1 (chi-sq., 1df, =5.5, 0.05>P>0.01) than a 3:1(chi-sq., 1df, =32, P<0.001) ratio. Such a segregation ratio suggestedthat a homozygous class of kanamycin resistant seedlings was absent fromthe progeny of KO.G374 plant. G374 can be a herbicide target.

Closely Related Genes from Other Species

Similar sequences to G374 are present in tomato and Medicago truncatula,and these sequences can be orthologs.

Example VIII Identification of Homologous Sequences

Homologous sequences from Arabidopsis and plant species other thanArabidopsis were identified using database sequence search tools, suchas the Basic Local Alignment Search Tool (BLAST) (Altschul et al. (1990)J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucl. Acid Res.25: 3389-3402). The tblastx sequence analysis programs were employedusing the BLOSUM-62 scoring matrix (Henikoff, S, and Henikoff, J. G.(1992) Proc. Natl. Acad. Sci. USA 89: 10915-10919).

Identified non-Arabidopsis sequences homologous to the Arabidopsissequences are provided in Table 4. The percent sequence identity amongthese sequences can be as low as 47%, or even lower sequence identity.The entire NCBI GenBank database was filtered for sequences from allplants except Arabidopsis thaliana by selecting all entries in the NCBIGenBank database associated with NCBI taxonomic ID 33090 (Viridiplantae;all plants) and excluding entries associated with taxonomic ID 3701(Arabidopsis thaliana). These sequences are compared to sequencesrepresenting genes of SEQ IDs NOs:2-2N, where N=2-561, using theWashington University TBLASTX algorithm (version 2.0a19 MP) at thedefault settings using gapped alignments with the filter “off”. For eachgene of SEQ IDs NOs:2-2N, where N=2-561, individual comparisons wereordered by probability score (P-value), where the score reflects theprobability that a particular alignment occurred by chance. For example,a score of 3.6e-40 is 3.6×10⁻⁴⁰. In addition to P-values, comparisonswere also scored by percentage identity. Percentage identity reflectsthe degree to which two segments of DNA or protein are identical over aparticular length. Examples of sequences so identified are presented inTable 4. Homologous or orthologous sequences are readily identified andavailable in GenBank by Accession number (Table 4; Test sequence ID) Theidentified homologous polynucleotide and polypeptide sequences andhomologues of the Arabidopsis polynucleotides and polypeptides may beorthologs of the Arabidopsis polynucleotides and polypeptides. (TBD: tobe determined.)

Example IX Introduction of Polynucleotides into Dicotyledonous Plants

SEQ ID NOs:1-(2N−1), wherein N=2-561, paralogous, orthologous, andhomologous sequences recombined into pMEN20 or pMEN65 expression vectorsare transformed into a plant for the purpose of modifying plant traits.The cloning vector may be introduced into a variety of cereal plants bymeans well-known in the art such as, for example, direct DNA transfer orAgrobacterium tumefaciens-mediated transformation. It is now routine toproduce transgenic plants using most dicot plants (see Weissbach andWeissbach, (1989) supra; Gelvin et al., (1990) supra; Herrera-Estrellaet al. (1983) supra; Bevan (1984) supra; and Klee (1985) supra). Methodsfor analysis of traits are routine in the art and examples are disclosedabove.

Example X Transformation of Cereal Plants with an Expression Vector

Cereal plants such as corn, wheat, rice, sorghum or barley, may also betransformed with the present polynucleotide sequences in pMEN20 orpMEN65 expression vectors for the purpose of modifying plant traits. Forexample, pMEN020 may be modified to replace the NptII coding region withthe BAR gene of Streptomyces hygroscopicus that confers resistance tophosphinothricin. The KpnI and BglII sites of the Bar gene are removedby site-directed mutagenesis with silent codon changes.

The cloning vector may be introduced into a variety of cereal plants bymeans well-known in the art such as, for example, direct DNA transfer orAgrobacterium tumefaciens-mediated transformation. It is now routine toproduce transgenic plants of most cereal crops (Vasil, I., Plant Molec.Biol. 25: 925-937 (1994)) such as corn, wheat, rice, sorghum (Cassas, A.et al., Proc. Natl. Acad Sci USA 90: 11212-11216 (1993) and barley (Wan,Y. and Lemeaux, P. Plant Physiol. 104:37-48 (1994). DNA transfer methodssuch as the microprojectile can be used for corn (Fromm. et al.Bio/Technology 8: 833-839 (1990); Gordon-Kamm et al. Plant Cell 2:603-618 (1990); Ishida, Y., Nature Biotechnology 14:745-750 (1990)),wheat (Vasil, et al. Bio/Technology 10:667-674 (1992); Vasil et al.,Bio/Technology 11: 1553-1558 (1993); Weeks et al., Plant Physiol.102:1077-1084 (1993)), rice (Christou Bio/Technology 9:957-962 (1991);Hiei et al. Plant J. 6:271-282 (1994); Aldemita and Hodges, Planta199:612-617; Hiei et al., Plant Mol. Biol. 35:205-18 (1997)). For mostcereal plants, embryogenic cells derived from immature scutellum tissuesare the preferred cellular targets for transformation (Hiei et al.,Plant Mol. Biol. 35:205-18 (1997); Vasil, Plant Molec. Biol. 25: 925-937(1994)).

Vectors according to the present invention may be transformed into cornembryogenic cells derived from immature scutellar tissue by usingmicroprojectile bombardment, with the A188XB73 genotype as the preferredgenotype (Fromm, et al., Bio/Technology 8: 833-839 (1990); Gordon-Kammet al., Plant Cell 2: 603-618 (1990)). After microprojectile bombardmentthe tissues are selected on phosphinothricin to identify the transgenicembryogenic cells (Gordon-Kamm et al., Plant Cell 2: 603-618 (1990)).Transgenic plants are regenerated by standard corn regenerationtechniques (Fromm, et al., Bio/Technology 8: 833-839 (1990); Gordon-Kammet al., Plant Cell 2: 603-618 (1990)).

The plasmids prepared as described above can also be used to producetransgenic wheat and rice plants (Christou, Bio/Technology 9:957-962(1991); Hiei et al., Plant J. 6:271-282 (1994); Aldemita and Hodges,Planta 199:612-617 (1996); Hiei et al., Plant Mol. Biol. 35:205-18(1997)) that coordinately express genes of interest by followingstandard transformation protocols known to those skilled in the art forrice and wheat Vasil, et al. Bio/Technology 10:667-674 (1992); Vasil etal., Bio/Technology 11:1553-1558 (1993); Weeks et al., Plant Physiol.102:1077-1084 (1993)), where the bar gene is used as the selectablemarker.

All references, publications, patent documents, web pages, and otherdocuments cited or mentioned herein are hereby incorporated by referencein their entirety for all purposes. Although the invention has beendescribed with reference to specific embodiments and examples, it shouldbe understood that one of ordinary skill can make various modificationswithout departing from the spirit of the invention. The scope of theinvention is not limited to the specific embodiments and examplesprovided.

1. A transgenic plant transformed with a recombinant polynucleotide thatencodes a polypeptide, wherein: the polypeptide has an amino acidsequence that is at least 90% identical to the conserved domain of aminoacids 175-245 of SEQ ID NO: 238; and overexpression of the polypeptidein the transgenic plant results in the transgenic plant havingconstitutive photomorphogenesis relative to a wild-type or referenceplant of the same species.
 2. The transgenic plant of claim 1, whereinthe polypeptide has an amino acid sequence that is at least 95%identical to the conserved domain of amino acids 175-245 of SEQ ID NO:238.
 3. The transgenic plant of claim 1, wherein the polypeptide has anamino acid sequence that is at least 98% identical to the conserveddomain of amino acids 175-245 of SEQ ID NO:
 238. 4. The transgenic plantof claim 1, wherein the polypeptide comprises SEQ ID NO:
 238. 5. Thetransgenic plant of claim 1, wherein the recombinant polynucleotidecomprises a constitutive, inducible, or tissue-specific promoter, andexpression of the polypeptide in the transgenic plant is regulated bythe constitutive, inducible, or tissue-specific promoter.
 6. Thetransgenic plant of claim 1, wherein the transgenic plant is a monocot.7. The transgenic plant of claim 1, wherein the transgenic plant is adicot.
 8. The transgenic plant of claim 1, wherein a progeny plantgerminated from a transformed seed produced by the transgenic plantexhibits constitutive photomorphogenesis as compared to the wild-type orreference plant.
 9. A transgenic plant transformed with a recombinantpolynucleotide that encodes a polypeptide, wherein: the polypeptide hasan amino acid sequence that is at least 90% identical to the conserveddomain of amino acids 175-245 of SEQ ID NO: 238; and overexpression ofthe polypeptide in the transgenic plant results in the transgenic planthaving early flowering relative to a wild-type or reference plant of thesame species.
 10. The transgenic plant of claim 9, wherein thepolypeptide has an amino acid sequence that is at least 95% identical tothe conserved domain of amino acids 175-245 of SEQ ID NO:
 238. 11. Thetransgenic plant of claim 9, wherein the polypeptide has an amino acidsequence that is at least 98% identical to the conserved domain of aminoacids 175-245 of SEQ ID NO:
 238. 12. The transgenic plant of claim 9,wherein the polypeptide comprises SEQ ID NO:
 238. 13. The transgenicplant of claim 9, wherein the recombinant polynucleotide comprises aconstitutive, inducible, or tissue-specific promoter, and expression ofthe polypeptide in the transgenic plant is regulated by theconstitutive, inducible, or tissue-specific promoter.
 14. The transgenicplant of claim 9, wherein the transgenic plant is a monocot.
 15. Thetransgenic plant of claim 9, wherein the transgenic plant is a dicot.16. A progeny plant germinated from a transformed seed produced by thetransgenic plant of claim 9, wherein the progeny plant has earlierflowering as compared to the wild-type or reference plant.
 17. A methodfor producing a transgenic plant that has constitutivephotomorphogenesis or early flowering relative to a wild-type orreference plant, the method steps comprising: (a) selecting apolynucleotide encoding a polypeptide, wherein the polypeptide has anamino acid sequence that is at least 90% identical to the conserveddomain of amino acids 175-245 of SEQ ID NO: 238; (b) inserting thepolynucleotide into a DNA construct; and (c) introducing the DNAconstruct into a plant or a plant cell to overexpress the polypeptideencoded by the polynucleotide; wherein when the polypeptide isoverexpressed in the transgenic plant, the polypeptide confers to thetransgenic plant constitutive photomorphogenesis or early floweringrelative to the wild-type or reference plant.
 18. The method of claim17, wherein the polypeptide has an amino acid sequence that is at least95% identical to the conserved domain of amino acids 175-245 of SEQ IDNO:
 238. 19. The method of claim 17, wherein the polypeptide has anamino acid sequence that is at least 98% identical to the conserveddomain of amino acids 175-245 of SEQ ID NO:
 238. 20. The method of claim17, wherein the polypeptide comprises SEQ ID NO:
 238. 21. The method ofclaim 17, wherein expression of the polypeptide is regulated by aconstitutive, inducible, or tissue-specific promoter.